Extremely fast linkage map construction for qtl objects using MSTmap.
mstmap.cross.RdExtremely fast linkage map construction for qtl objects using the source code for MSTmap (see Wu et al., 2008). The construction includes linkage group clustering, marker ordering and genetic distance calculations.
Usage
# S3 method for class 'cross'
mstmap(object, chr, id = "Genotype", bychr = TRUE,
suffix = "numeric", anchor = FALSE, dist.fun = "kosambi",
objective.fun = "COUNT", p.value = 1e-06, noMap.dist = 15,
noMap.size = 0, miss.thresh = 1, mvest.bc = FALSE,
detectBadData = FALSE, return.imputed = FALSE,
trace = FALSE, ...)Arguments
- object
A
"cross"object generated from the qtl package. Specifically the object needs to inherit from one of the following classes"bc","dh","riself","bcsft"(see Details).- chr
A character string of linkage group names that require re-construction and/or optimal ordering of the markers they contain. (see Details).
- id
The name of the column in
object$phenothat uniquely identifies the genotype names. Default is"Genotype".- bychr
Logical value. For a given set of linkage groups defined by
chr, ifTRUEthen split linkage groups (only if required, seep.value) and order markers within linkage groups. IfFALSEthen combine linkage groups and reconstruct. Default isTRUE.- suffix
Character string either
"numeric"or"alpha"determining whether numeric or alphabetic ascending values are post-fixed to linkage group names when splitting linkage groups.- anchor
Logical value. The MSTmap algorithm does not respect the inputted marker order of the linkage map required for construction. For a given set of linkage groups defined by
chr, ifTRUEthe order of the inputted markers is respected regardless of the choices ofchrandbychr. Default isFALSE.- dist.fun
Character string defining the distance function used for calculation of genetic distances. Options are "kosambi" and "haldane". Default is "kosambi".
- objective.fun
Character string defining the objective function to be used when constructing the map. Options are
"COUNT"for minimising the sum of recombination events between markers and"ML"for maximising the likelihood objective function. Default is"COUNT".- p.value
Numerical value to specify the threshold to use when clustering markers. Defaults to
1e-06. If a value greater than one is given this feature is turned off inputted marker data are assumed to belong to the same linkage group (see Details).- noMap.dist
Numerical value to specify the smallest genetic distance a set of isolated markers can appear distinct from other linked markers. Isolated markers will appear in their own linkage groups and will be of size specified by
noMap.size.- noMap.size
Numerical value to specify the maximum size of isolated marker linkage groups that have been identified using
noMap.dist. This feature can be turned off by setting it to 0. Default is 0.- miss.thresh
Numerical value to specify the threshold proportion of missing marker scores allowable in each of the markers. Markers above this threshold will not be included in the linkage map. Default is 1.
- mvest.bc
Logical value. If
TRUEmissing markers will be imputed before clustering the markers into linkage groups. This is restricted to"bc","dh","riself"populations only (see Details). Default isFALSE.- detectBadData
Logical value. If
TRUEpossible genotyping errors are detected, set to missing and then imputed as part of the marker ordering algorithm. Genotyping errors will also be printed in the file specified bytrace. This is restricted to"bc","dh","riself"populations only. (see Details). Default isFALSE.- return.imputed
Logical value. If
TRUEthen the imputed marker probability matrix is returned for the linkage groups that are constructed (see Details). Default isFALSE.- trace
An automatic tracing facility. If
trace = FALSEthen minimalMSTmapoutput is piped to the screen during the algorithm. Iftrace = TRUE, then detailed output from MSTmap is piped to"MSToutput.txt". This file is equivalent to the output that would be obtained from running the MSTmap executable from the command line.- ...
Currently ignored.
Details
The qtl cross object needs to inherit one of the allowable classes
"bc","dh","riself", "bcsft". This provides a safeguard against
attempts to construct a map for more complex populations that can
exist in qtl. Users should be aware when doubled haploid
populations are read in using read.cross() from the qtl
package they inherit the class "bc". Users can apply the class
"dh" by simply changing the class of the object. For the purpose
of linkage map construction the classes "bc" and "dh" will
provide equivalent results.
MSTmap supports "RILn" populations, where n is the number of generations
of selfing. Markers in these populations are required to be fully
informative i.e. contain 3 distinct allele types such as AA, BB for
parental homozygotes and AB for phase unknown heterozygotes.
If read.cross is used to import the "RILn" population the resultant
object will initially be given a class "f2". The level of selfing
would then have to be encoded into the object by applying one of the two conversion
functions available in the qtl package. For a
population that has been generated by selfing n times the conversion
function convert2bcsft can be used by setting the arguments
F.gen = n and BC.gen = 0. Populations that are genuine
advanced RILs can be converted using the convert2riself function.
This method function is designed to be an "all-in-one" function that
will allow you to construct linkage maps extremely fast in multiple
different ways from the supplied cross object. Initially, the map
can be kept complete or a subset of selected linkage groups can be chosen
using the chr argument. Setting bychr = FALSE will
bulk the marker information for the selected linkage groups and, if
necessary, form new linkage groups and optimise the marker order within
each. Setting bychr = TRUE will ensure that markers
are optimally ordered within each linkage group. This will also break
linkage groups depending on the p-value given in the call (see
below for details of the use of p.value). If the
linkage map was initially subsetted, the linkage groups not involved in
the subset are returned to ensure the map is complete.
The algorithm allows an adjustment of the p.value threshold for
clustering of markers to distinct linkage groups (see Wu et al.,
2008) and is highly dependent on the number of individuals in
the population. As the number of individuals increases the
p.value threshold should be decreased accordingly. This may
require some trial and error to achieve desired results.
When bychr = TRUE, established linkage groups may also split
depending on the p.value given. To prevent this the p.value threshold
may be increased to a desired value or the splitting may be prevented
altogether by supplying a value greater than one to this argument.
If mvest.bc = TRUE and the population type is "bc","dh","riself"
then missing values are imputed before markers are clustered into
linkage groups. This is only a simple imputation that places a 0.5
probability of the missing observation being one allele or the other and
is used to assist the clustering algorithm when there is known to be high numbers of
missing observations between pairs of markers.
It should be highlighted that for population types
"bc","dh","riself", imputation of missing values occurs
regardless of the value of mvest.bc. This is achieved using an EM algorithm that is
tightly coupled with marker ordering (see Wu et al., 2008). Initially
a marker order is obtained omitting missing marker scores and then
imputation is performed based on the underlying recombinant probabilities
of the flanking markers with the markers containing the missing
value. The recombinant probabilities are then recomputed and an update of
the pairwise distances are calculated. The ordering algorithm is then
run again and the complete process is repeated until
convergence. Note, the imputed probability matrix for the linkage map
being constructed is returned if return.imputed = TRUE.
For populations "bc","dh","riself", if detectBadData =
TRUE the marker ordering algorithm also
includes the detection of genotyping errors. For any individual
genotype, the detection method is based on a weighted Euclidean metric
(see Wu et al., 2008) that is a function of the
recombination probabilities of all the markers with the marker containing
the suspicious observation. Any genotyping errors detected are set to
missing and the missing values are then imputed as part of the marker
ordering algorithm. Note, the detection of these errors and their
amendment can be returned in the imputed probability matrix if
return.imputed = TRUE.
If return.imputed = TRUE and the object has class
"bc","dh","riself" then the marker probability matrix is
returned for the linkage groups that have been constructed using the
algorithm. Each linkage group is named identically to the linkage groups
of the map and contains an ordered "map" element and a "data"
element consisting of marker probabilities of the A allele being
present (i.e. P(A) = 1, P(B) = 0). Both elements contain a
possibly reduced version of the marker set that includes all
non-colocating markers as well as the first marker of any set of
co-locating markers.
Value
The function returns a cross object with an identical class
structure to the cross object inputted. The object is a list
with usual components "pheno" and "geno". If markers were
omitted for any reason during the construction, the object will have an
"omit" component with all omitted markers in a collated
matrix. If return.imputed = TRUE then the object will also
contain an "imputed.geno" element.
References
Wu, Y., Bhat, P., Close, T.J, Lonardi, S. (2008) Efficient and Accurate Construction of Genetic Linkage Maps from Minimum Spanning Tree of a Graph. Plos Genetics, 4, Issue 10.
Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.
Examples
data(mapDH, package = "ASMap")
## bulking linkage groups and reconstructing entire linkage map
test1 <- mstmap(mapDH, bychr = FALSE, dist.fun = "kosambi",
trace = FALSE)
#> Number of linkage groups: 24
#> The size of the linkage groups are: 41 5 33 10 40 35 8 13 37 30 6 9 21 32 6 54 56 6 27 41 15 33 37 4
#> The number of bins in each linkage group: 41 4 33 9 40 34 7 13 36 29 5 8 21 32 6 53 55 5 27 41 14 32 36 3
pull.map(test1)
#> $L.1
#> 1A.m.41 1A.m.40 1A.m.39 1A.m.38 1A.m.37 1A.m.36
#> 0.0000000 0.4587285 0.9174569 3.2126457 10.1373152 11.5138097
#> 1A.m.35 1A.m.34 1A.m.33 1A.m.32 1A.m.31 1A.m.30
#> 16.1139008 23.9762340 24.4349625 24.8936909 25.9826349 27.1876743
#> 1A.m.29 1A.m.28 1A.m.27 1A.m.26 1A.m.25 1A.m.24
#> 29.0233610 32.2387955 32.6975239 34.5332107 63.5518124 64.9283068
#> 1A.m.23 1A.m.22 1A.m.21 1A.m.20 1A.m.19 1A.m.18
#> 68.1437413 68.6024697 69.0611982 69.9787324 71.3552268 71.8139553
#> 1A.m.17 1A.m.16 1A.m.15 1A.m.13 1A.m.14 1A.m.12
#> 72.7314894 73.1902179 74.5667123 75.5029664 75.9804099 76.4391384
#> 1A.m.11 1A.m.10 1A.m.9 1A.m.8 1A.m.7 1A.m.6
#> 77.8156328 78.7331670 81.4882455 81.9469740 82.4057024 82.8644309
#> 1A.m.5 1A.m.4 1A.m.3 1A.m.2 1A.m.1
#> 83.3231594 84.6996538 99.8235155 102.5785940 103.9550885
#>
#> $L.10
#> 3B.m.30 3B.m.29 3B.m.28 3B.m.27 3B.m.26 3B.m.25 3B.m.24 3B.m.23
#> 0.00000 10.23223 22.39308 30.25542 34.39367 34.85278 38.99064 53.45212
#> 3B.m.22 3B.m.21 3B.m.20 3B.m.19 3B.m.17 3B.m.18 3B.m.16 3B.m.15
#> 56.35658 61.41969 66.48280 67.40033 68.31786 68.77659 69.23532 69.69405
#> 3B.m.14 3B.m.13 3B.m.11 3B.m.12 3B.m.10 3B.m.9 3B.m.8 3B.m.7
#> 73.83191 74.29064 74.74937 74.74937 75.20810 97.15983 98.07737 104.62584
#> 3B.m.6 3B.m.5 3B.m.4 3B.m.3 3B.m.2 3B.m.1
#> 129.29707 131.59226 132.05099 132.50972 133.42725 133.88598
#>
#> $L.11
#> 3D.m.6 3D.m.5 3D.m.4 3D.m.3 3D.m.1 3D.m.2
#> 0.0000000 0.4587314 5.0589782 8.2768742 8.7379031 8.7379031
#>
#> $L.12
#> 4A.m.9 4A.m.7 4A.m.8 4A.m.6 4A.m.5 4A.m.3 4A.m.4 4A.m.2
#> 0.000000 1.835687 1.835687 2.294415 2.753144 3.670678 4.129406 6.424595
#> 4A.m.1
#> 7.801089
#>
#> $L.13
#> 4A.m.30 4A.m.29 4A.m.28 4A.m.27 4A.m.26 4A.m.25 4A.m.24 4A.m.23
#> 0.00000 6.92467 18.60024 26.93343 43.06735 44.44384 44.90257 45.82010
#> 4A.m.22 4A.m.21 4A.m.20 4A.m.19 4A.m.18 4A.m.17 4A.m.16 4A.m.15
#> 46.73764 47.19637 48.11390 51.79024 53.16673 53.62546 83.92398 84.38271
#> 4A.m.14 4A.m.13 4A.m.12 4A.m.11 4A.m.10
#> 86.67790 94.54023 94.99896 95.91650 98.21169
#>
#> $L.14
#> 4B.m.32 4B.m.31 4B.m.30 4B.m.29 4B.m.28 4B.m.27 4B.m.26
#> 0.000000 8.333189 21.963866 22.881400 24.257894 29.784884 37.647217
#> 4B.m.25 4B.m.24 4B.m.23 4B.m.22 4B.m.21 4B.m.20 4B.m.19
#> 41.785078 42.243806 43.161340 50.086010 51.003544 52.380039 52.838767
#> 4B.m.18 4B.m.17 4B.m.16 4B.m.15 4B.m.14 4B.m.13 4B.m.12
#> 53.756301 56.051490 56.510218 58.345905 58.804634 59.263362 59.722091
#> 4B.m.11 4B.m.10 4B.m.9 4B.m.8 4B.m.7 4B.m.6 4B.m.5
#> 60.180819 60.639547 61.557082 62.015810 64.310999 78.436651 81.191729
#> 4B.m.4 4B.m.3 4B.m.2 4B.m.1
#> 83.946808 91.340123 91.799300 109.472825
#>
#> $L.15
#> 4D.m.6 4D.m.5 4D.m.4 4D.m.3 4D.m.2 4D.m.1
#> 0.000000 4.600091 8.776795 10.651111 12.143891 13.255588
#>
#> $L.16
#> 5A.m.54 5A.m.53 5A.m.52 5A.m.51 5A.m.50 5A.m.49
#> 0.0000000 0.4587285 0.9174569 1.8376979 19.5108820 38.7568771
#> 5A.m.48 5A.m.47 5A.m.46 5A.m.45 5A.m.44 5A.m.43
#> 39.2156055 41.0512923 49.8568071 50.3155356 50.7742640 51.2329925
#> 5A.m.42 5A.m.41 5A.m.40 5A.m.39 5A.m.38 5A.m.36
#> 51.6917210 53.0682154 58.1313220 58.5900505 60.4257372 61.8022316
#> 5A.m.37 5A.m.35 5A.m.34 5A.m.33 5A.m.32 5A.m.31
#> 61.8022316 62.2609601 63.1784942 66.3939287 69.1490072 70.0665414
#> 5A.m.30 5A.m.29 5A.m.28 5A.m.27 5A.m.26 5A.m.25
#> 70.5252698 72.3609565 73.7374510 74.1961794 76.0318662 79.7082016
#> 5A.m.24 5A.m.23 5A.m.22 5A.m.21 5A.m.20 5A.m.19
#> 80.1669301 86.1587514 87.0762856 100.7069618 105.7700684 106.2287969
#> 5A.m.18 5A.m.17 5A.m.16 5A.m.15 5A.m.14 5A.m.13
#> 106.6875254 108.0640198 109.4405142 117.7737037 119.6093904 123.7472514
#> 5A.m.12 5A.m.10 5A.m.11 5A.m.9 5A.m.8 5A.m.7
#> 128.3473425 130.6425312 131.1012597 160.1198614 166.1116828 171.1747894
#> 5A.m.6 5A.m.5 5A.m.4 5A.m.3 5A.m.2 5A.m.1
#> 172.0923235 172.5510520 173.0097805 174.8454672 175.3041956 181.7618822
#>
#> $L.17
#> 5B.m.56 5B.m.55 5B.m.54 5B.m.53 5B.m.52 5B.m.51
#> 0.0000000 0.9175342 14.0558285 17.7321639 20.0273526 20.4860811
#> 5B.m.50 5B.m.49 5B.m.48 5B.m.47 5B.m.46 5B.m.45
#> 22.3217678 22.7804963 23.2392247 23.6979532 24.1566817 24.6154101
#> 5B.m.44 5B.m.43 5B.m.42 5B.m.41 5B.m.40 5B.m.39
#> 25.0741386 25.9916728 26.4504012 26.9091297 27.3678582 27.8265933
#> 5B.m.38 5B.m.37 5B.m.36 5B.m.35 5B.m.34 5B.m.33
#> 28.7680562 29.2508125 31.5461135 32.0048420 32.4635705 33.3811046
#> 5B.m.32 5B.m.31 5B.m.29 5B.m.30 5B.m.28 5B.m.27
#> 33.8398331 34.7573673 36.1338617 36.5925902 37.0513186 60.1193592
#> 5B.m.26 5B.m.25 5B.m.24 5B.m.23 5B.m.22 5B.m.21
#> 64.2572202 64.7159486 65.1746771 66.5511715 72.0781607 75.2935951
#> 5B.m.20 5B.m.19 5B.m.18 5B.m.17 5B.m.15 5B.m.16
#> 76.7000704 78.6053647 79.5624655 83.2388010 83.6975294 83.6975294
#> 5B.m.14 5B.m.13 5B.m.12 5B.m.11 5B.m.10 5B.m.9
#> 98.3208693 98.7795978 111.9178921 112.8354262 115.5905047 120.6536113
#> 5B.m.8 5B.m.7 5B.m.6 5B.m.5 5B.m.4 5B.m.3
#> 125.2537024 125.7124309 135.4673718 137.7625605 138.6800947 139.6333935
#> 5B.m.2 5B.m.1
#> 142.1178003 142.7883741
#>
#> $L.18
#> 5D.m.6 5D.m.4 5D.m.5 5D.m.1 5D.m.2 5D.m.3
#> 0.0000000 0.4587285 0.4587285 17.1024336 17.5611621 18.0198906
#>
#> $L.19
#> 6A.m.27 6A.m.26 6A.m.25 6A.m.24 6A.m.23 6A.m.22 6A.m.21
#> 0.0000000 0.4587285 3.2138070 3.6725354 4.5900696 29.3742386 37.2365718
#> 6A.m.20 6A.m.18 6A.m.19 6A.m.17 6A.m.16 6A.m.15 6A.m.14
#> 38.6130662 40.9082550 41.3669834 41.8257119 42.2844404 43.2019745 45.0376613
#> 6A.m.13 6A.m.12 6A.m.11 6A.m.10 6A.m.9 6A.m.8 6A.m.7
#> 51.9623308 56.1001918 63.9625251 65.3494460 74.1657062 74.6244347 79.6875413
#> 6A.m.6 6A.m.5 6A.m.4 6A.m.3 6A.m.2 6A.m.1
#> 91.3631163 93.1988030 95.0344897 97.3296785 98.2472126 98.7059411
#>
#> $L.2
#> 1B1.m.4 1B1.m.5 1B1.m.3 1B1.m.2 1B1.m.1
#> 0.000000 0.000000 4.137861 6.892939 7.810474
#>
#> $L.20
#> 6B.m.41 6B.m.40 6B.m.39 6B.m.38 6B.m.37 6B.m.36 6B.m.35
#> 0.000000 3.228588 4.666779 7.462087 9.716855 10.674985 11.133714
#> 6B.m.34 6B.m.33 6B.m.32 6B.m.31 6B.m.30 6B.m.29 6B.m.28
#> 13.428903 20.821759 23.152283 26.403125 43.559982 46.315061 46.773789
#> 6B.m.27 6B.m.26 6B.m.25 6B.m.24 6B.m.23 6B.m.22 6B.m.21
#> 47.232518 47.694728 55.553493 56.012221 58.767300 60.143794 60.602523
#> 6B.m.20 6B.m.19 6B.m.18 6B.m.16 6B.m.17 6B.m.15 6B.m.14
#> 62.438210 63.923978 64.732295 65.649829 66.108558 66.567286 67.943781
#> 6B.m.13 6B.m.12 6B.m.11 6B.m.10 6B.m.9 6B.m.8 6B.m.7
#> 68.402509 69.320043 73.457904 80.382574 80.841302 81.300031 101.078220
#> 6B.m.6 6B.m.5 6B.m.4 6B.m.2 6B.m.3 6B.m.1
#> 110.357621 110.816350 112.192844 114.488173 114.947042 115.406325
#>
#> $L.21
#> 6D.m.15 6D.m.14 6D.m.13 6D.m.12 6D.m.11 6D.m.10 6D.m.9
#> 0.0000000 0.9225051 4.1379396 10.6171243 39.6108758 57.8493328 58.7668670
#> 6D.m.8 6D.m.7 6D.m.6 6D.m.5 6D.m.4 6D.m.2 6D.m.3
#> 59.2262509 69.4591643 69.9178927 70.8354269 71.2941554 71.7528838 71.7528838
#> 6D.m.1
#> 72.2116123
#>
#> $L.22
#> 7A.m.32 7A.m.33 7A.m.31 7A.m.30 7A.m.29 7A.m.28 7A.m.27
#> 0.000000 0.000000 0.684333 4.106999 5.024533 5.488570 10.094015
#> 7A.m.26 7A.m.25 7A.m.24 7A.m.23 7A.m.22 7A.m.21 7A.m.20
#> 11.011549 18.873882 34.501225 36.796414 37.715916 47.472900 68.874166
#> 7A.m.19 7A.m.18 7A.m.17 7A.m.16 7A.m.15 7A.m.14 7A.m.13
#> 69.791700 70.709234 71.167963 72.085497 72.544226 73.920720 78.474431
#> 7A.m.12 7A.m.11 7A.m.10 7A.m.9 7A.m.8 7A.m.7 7A.m.6
#> 79.437975 80.814469 83.109658 84.027192 86.782271 87.240999 113.797115
#> 7A.m.5 7A.m.4 7A.m.3 7A.m.2 7A.m.1
#> 118.860222 127.193412 131.793503 133.796103 134.474614
#>
#> $L.23
#> 7B.m.37 7B.m.36 7B.m.35 7B.m.34 7B.m.33 7B.m.31 7B.m.32 7B.m.30
#> 0.00000 23.63430 24.09303 27.76936 29.14586 30.06339 30.52212 36.04911
#> 7B.m.29 7B.m.28 7B.m.27 7B.m.26 7B.m.25 7B.m.24 7B.m.23 7B.m.21
#> 38.80419 39.72172 58.43965 59.35718 62.57262 65.32769 65.78642 69.00186
#> 7B.m.22 7B.m.20 7B.m.19 7B.m.17 7B.m.18 7B.m.16 7B.m.15 7B.m.14
#> 69.00186 69.91939 72.67447 74.96966 75.42839 75.88712 76.80465 77.26338
#> 7B.m.13 7B.m.12 7B.m.11 7B.m.10 7B.m.9 7B.m.8 7B.m.6 7B.m.7
#> 79.55857 80.47610 81.39364 81.85236 82.31109 83.22863 84.60512 85.36757
#> 7B.m.5 7B.m.4 7B.m.3 7B.m.2 7B.m.1
#> 86.91130 92.42609 92.88482 98.87664 108.15604
#>
#> $L.24
#> 7D.m.4 7D.m.2 7D.m.3 7D.m.1
#> 0.000000 5.526989 5.526989 21.660902
#>
#> $L.3
#> 1B2.m.33 1B2.m.32 1B2.m.31 1B2.m.30 1B2.m.29 1B2.m.28 1B2.m.27 1B2.m.26
#> 0.000000 9.279401 10.655895 11.573429 12.032158 13.867845 15.289476 16.711107
#> 1B2.m.25 1B2.m.24 1B2.m.23 1B2.m.22 1B2.m.21 1B2.m.20 1B2.m.19 1B2.m.18
#> 17.169836 18.546330 19.463864 20.851965 29.173232 31.008919 32.844606 36.520941
#> 1B2.m.17 1B2.m.16 1B2.m.15 1B2.m.14 1B2.m.13 1B2.m.12 1B2.m.11 1B2.m.10
#> 36.979670 38.356164 38.814893 40.650579 42.027074 42.944608 43.862142 44.320871
#> 1B2.m.9 1B2.m.8 1B2.m.7 1B2.m.6 1B2.m.5 1B2.m.4 1B2.m.3 1B2.m.2
#> 44.779599 46.156094 47.991780 48.450509 49.827003 51.203498 51.662226 59.995416
#> 1B2.m.1
#> 60.912950
#>
#> $L.4
#> 1D.m.10 1D.m.9 1D.m.8 1D.m.7 1D.m.6 1D.m.5 1D.m.3 1D.m.4
#> 0.00000 22.50673 22.96620 23.88404 55.53218 59.75146 78.46976 78.46976
#> 1D.m.2 1D.m.1
#> 78.92881 81.22400
#>
#> $L.5
#> 2A.m.40 2A.m.39 2A.m.38 2A.m.37 2A.m.36 2A.m.35 2A.m.34
#> 0.000000 2.654039 3.575343 4.953997 5.872637 7.249131 18.886363
#> 2A.m.33 2A.m.32 2A.m.31 2A.m.30 2A.m.29 2A.m.28 2A.m.26
#> 24.338629 24.797357 29.860464 30.319193 45.946535 46.885701 49.640780
#> 2A.m.27 2A.m.25 2A.m.24 2A.m.23 2A.m.22 2A.m.21 2A.m.20
#> 51.476466 52.394000 54.689189 57.904624 58.363352 58.822081 62.959942
#> 2A.m.19 2A.m.18 2A.m.17 2A.m.16 2A.m.15 2A.m.14 2A.m.13
#> 63.418670 76.067061 77.902748 80.657826 83.412910 83.886982 84.345711
#> 2A.m.12 2A.m.11 2A.m.10 2A.m.9 2A.m.8 2A.m.7 2A.m.6
#> 84.804439 85.263167 85.721896 101.855809 105.993670 106.452398 111.979387
#> 2A.m.5 2A.m.4 2A.m.3 2A.m.2 2A.m.1
#> 126.105039 127.940726 128.858260 138.613201 153.236541
#>
#> $L.6
#> 2B.m.35 2B.m.33 2B.m.34 2B.m.31 2B.m.32 2B.m.30 2B.m.29 2B.m.28
#> 0.00000 16.64371 17.10243 18.47893 18.47893 18.93766 19.39638 19.85511
#> 2B.m.27 2B.m.26 2B.m.25 2B.m.24 2B.m.23 2B.m.22 2B.m.21 2B.m.20
#> 20.77265 21.69018 22.14891 23.98460 24.44333 25.81982 27.19631 27.65504
#> 2B.m.19 2B.m.18 2B.m.17 2B.m.16 2B.m.15 2B.m.14 2B.m.13 2B.m.12
#> 29.03154 29.94907 30.86661 31.32533 31.78406 32.24279 33.61929 35.45497
#> 2B.m.11 2B.m.10 2B.m.9 2B.m.8 2B.m.7 2B.m.6 2B.m.5 2B.m.4
#> 36.37251 45.17802 45.63675 46.09548 47.93116 56.26435 65.54376 71.07074
#> 2B.m.3 2B.m.2 2B.m.1
#> 71.52947 94.59751 97.37680
#>
#> $L.7
#> 2D1.m.8 2D1.m.6 2D1.m.7 2D1.m.5 2D1.m.4 2D1.m.3 2D1.m.2 2D1.m.1
#> 0.00000 13.13829 13.13829 16.77185 17.73195 18.20947 18.71471 19.20363
#>
#> $L.8
#> 2D2.m.13 2D2.m.12 2D2.m.11 2D2.m.9 2D2.m.10 2D2.m.8 2D2.m.7 2D2.m.6
#> 0.000000 3.215434 10.137247 11.057585 11.516314 42.462800 46.604503 47.066011
#> 2D2.m.5 2D2.m.4 2D2.m.3 2D2.m.2 2D2.m.1
#> 49.363984 51.660473 59.519642 59.982755 60.441483
#>
#> $L.9
#> 3A.m.37 3A.m.35 3A.m.36 3A.m.34 3A.m.33 3A.m.32
#> 0.0000000 0.4587285 0.4587285 1.8352229 2.2939514 4.5891402
#> 3A.m.31 3A.m.30 3A.m.29 3A.m.28 3A.m.27 3A.m.26
#> 5.5066743 7.4768940 15.9172288 26.6285944 38.3224121 44.3317651
#> 3A.m.25 3A.m.24 3A.m.23 3A.m.22 3A.m.21 3A.m.20
#> 50.7894517 56.7812731 57.2400015 63.6976881 64.6152223 65.5327565
#> 3A.m.19 3A.m.16 3A.m.17 3A.m.18 3A.m.15 3A.m.14
#> 68.7481909 82.8738429 83.7913771 84.2501056 85.6266000 86.0853285
#> 3A.m.13 3A.m.10 3A.m.9 3A.m.11 3A.m.12 3A.m.8
#> 86.5440569 90.6819179 92.0584123 93.4349067 95.7300955 126.0286198
#> 3A.m.7 3A.m.6 3A.m.5 3A.m.4 3A.m.3 3A.m.2
#> 126.9461540 133.4038406 134.3213748 137.9977120 144.9223833 145.3811118
#> 3A.m.1
#> 145.8398402
#>
## one linkage group at a time (possibly break established linkage
## groups)
test2 <- mstmap(mapDH, bychr = TRUE, dist.fun = "kosambi", trace = FALSE)
#> Number of linkage groups: 1
#> The size of the linkage groups are: 41
#> The number of bins in each linkage group: 41
#> Number of linkage groups: 1
#> The size of the linkage groups are: 5
#> The number of bins in each linkage group: 4
#> Number of linkage groups: 1
#> The size of the linkage groups are: 33
#> The number of bins in each linkage group: 33
#> Number of linkage groups: 1
#> The size of the linkage groups are: 10
#> The number of bins in each linkage group: 9
#> Number of linkage groups: 1
#> The size of the linkage groups are: 40
#> The number of bins in each linkage group: 40
#> Number of linkage groups: 1
#> The size of the linkage groups are: 35
#> The number of bins in each linkage group: 34
#> Number of linkage groups: 1
#> The size of the linkage groups are: 8
#> The number of bins in each linkage group: 7
#> Number of linkage groups: 1
#> The size of the linkage groups are: 13
#> The number of bins in each linkage group: 13
#> Number of linkage groups: 1
#> The size of the linkage groups are: 37
#> The number of bins in each linkage group: 36
#> Number of linkage groups: 1
#> The size of the linkage groups are: 30
#> The number of bins in each linkage group: 29
#> Number of linkage groups: 1
#> The size of the linkage groups are: 6
#> The number of bins in each linkage group: 5
#> Number of linkage groups: 2
#> The size of the linkage groups are: 9 21
#> The number of bins in each linkage group: 8 21
#> Number of linkage groups: 1
#> The size of the linkage groups are: 32
#> The number of bins in each linkage group: 32
#> Number of linkage groups: 1
#> The size of the linkage groups are: 6
#> The number of bins in each linkage group: 6
#> Number of linkage groups: 1
#> The size of the linkage groups are: 54
#> The number of bins in each linkage group: 53
#> Number of linkage groups: 1
#> The size of the linkage groups are: 56
#> The number of bins in each linkage group: 55
#> Number of linkage groups: 1
#> The size of the linkage groups are: 6
#> The number of bins in each linkage group: 5
#> Number of linkage groups: 1
#> The size of the linkage groups are: 27
#> The number of bins in each linkage group: 27
#> Number of linkage groups: 1
#> The size of the linkage groups are: 41
#> The number of bins in each linkage group: 41
#> Number of linkage groups: 1
#> The size of the linkage groups are: 15
#> The number of bins in each linkage group: 14
#> Number of linkage groups: 1
#> The size of the linkage groups are: 33
#> The number of bins in each linkage group: 32
#> Number of linkage groups: 1
#> The size of the linkage groups are: 37
#> The number of bins in each linkage group: 36
#> Number of linkage groups: 1
#> The size of the linkage groups are: 4
#> The number of bins in each linkage group: 3
pull.map(test2)
#> $`1A`
#> 1A.m.41 1A.m.40 1A.m.39 1A.m.38 1A.m.37 1A.m.36
#> 0.0000000 0.4587285 0.9174569 3.2126457 10.1373152 11.5138097
#> 1A.m.35 1A.m.34 1A.m.33 1A.m.32 1A.m.31 1A.m.30
#> 16.1139008 23.9762340 24.4349625 24.8936909 25.9826349 27.1876743
#> 1A.m.29 1A.m.28 1A.m.27 1A.m.26 1A.m.25 1A.m.24
#> 29.0233610 32.2387955 32.6975239 34.5332107 63.5518124 64.9283068
#> 1A.m.23 1A.m.22 1A.m.21 1A.m.20 1A.m.19 1A.m.18
#> 68.1437413 68.6024697 69.0611982 69.9787324 71.3552268 71.8139553
#> 1A.m.17 1A.m.16 1A.m.15 1A.m.13 1A.m.14 1A.m.12
#> 72.7314894 73.1902179 74.5667123 75.5029664 75.9804099 76.4391384
#> 1A.m.11 1A.m.10 1A.m.9 1A.m.8 1A.m.7 1A.m.6
#> 77.8156328 78.7331670 81.4882455 81.9469740 82.4057024 82.8644309
#> 1A.m.5 1A.m.4 1A.m.3 1A.m.2 1A.m.1
#> 83.3231594 84.6996538 99.8235155 102.5785940 103.9550885
#>
#> $`1B1`
#> 1B1.m.4 1B1.m.5 1B1.m.3 1B1.m.2 1B1.m.1
#> 0.000000 0.000000 4.137861 6.892939 7.810474
#>
#> $`1B2`
#> 1B2.m.33 1B2.m.32 1B2.m.31 1B2.m.30 1B2.m.29 1B2.m.28 1B2.m.27 1B2.m.26
#> 0.000000 9.279401 10.655895 11.573429 12.032158 13.867845 15.289476 16.711107
#> 1B2.m.25 1B2.m.24 1B2.m.23 1B2.m.22 1B2.m.21 1B2.m.20 1B2.m.19 1B2.m.18
#> 17.169836 18.546330 19.463864 20.851965 29.173232 31.008919 32.844606 36.520941
#> 1B2.m.17 1B2.m.16 1B2.m.15 1B2.m.14 1B2.m.13 1B2.m.12 1B2.m.11 1B2.m.10
#> 36.979670 38.356164 38.814893 40.650579 42.027074 42.944608 43.862142 44.320871
#> 1B2.m.9 1B2.m.8 1B2.m.7 1B2.m.6 1B2.m.5 1B2.m.4 1B2.m.3 1B2.m.2
#> 44.779599 46.156094 47.991780 48.450509 49.827003 51.203498 51.662226 59.995416
#> 1B2.m.1
#> 60.912950
#>
#> $`1D`
#> 1D.m.10 1D.m.9 1D.m.8 1D.m.7 1D.m.6 1D.m.5 1D.m.3 1D.m.4
#> 0.00000 22.50673 22.96620 23.88404 55.53218 59.75146 78.46976 78.46976
#> 1D.m.2 1D.m.1
#> 78.92881 81.22400
#>
#> $`2A`
#> 2A.m.40 2A.m.39 2A.m.38 2A.m.37 2A.m.36 2A.m.35 2A.m.34
#> 0.000000 2.654039 3.575343 4.953997 5.872637 7.249131 18.886363
#> 2A.m.33 2A.m.32 2A.m.31 2A.m.30 2A.m.29 2A.m.28 2A.m.26
#> 24.338629 24.797357 29.860464 30.319193 45.946535 46.885701 49.640780
#> 2A.m.27 2A.m.25 2A.m.24 2A.m.23 2A.m.22 2A.m.21 2A.m.20
#> 51.476466 52.394000 54.689189 57.904624 58.363352 58.822081 62.959942
#> 2A.m.19 2A.m.18 2A.m.17 2A.m.16 2A.m.15 2A.m.14 2A.m.13
#> 63.418670 76.067061 77.902748 80.657826 83.412910 83.886982 84.345711
#> 2A.m.12 2A.m.11 2A.m.10 2A.m.9 2A.m.8 2A.m.7 2A.m.6
#> 84.804439 85.263167 85.721896 101.855809 105.993670 106.452398 111.979387
#> 2A.m.5 2A.m.4 2A.m.3 2A.m.2 2A.m.1
#> 126.105039 127.940726 128.858260 138.613201 153.236541
#>
#> $`2B`
#> 2B.m.35 2B.m.33 2B.m.34 2B.m.31 2B.m.32 2B.m.30 2B.m.29 2B.m.28
#> 0.00000 16.64371 17.10243 18.47893 18.47893 18.93766 19.39638 19.85511
#> 2B.m.27 2B.m.26 2B.m.25 2B.m.24 2B.m.23 2B.m.22 2B.m.21 2B.m.20
#> 20.77265 21.69018 22.14891 23.98460 24.44333 25.81982 27.19631 27.65504
#> 2B.m.19 2B.m.18 2B.m.17 2B.m.16 2B.m.15 2B.m.14 2B.m.13 2B.m.12
#> 29.03154 29.94907 30.86661 31.32533 31.78406 32.24279 33.61929 35.45497
#> 2B.m.11 2B.m.10 2B.m.9 2B.m.8 2B.m.7 2B.m.6 2B.m.5 2B.m.4
#> 36.37251 45.17802 45.63675 46.09548 47.93116 56.26435 65.54376 71.07074
#> 2B.m.3 2B.m.2 2B.m.1
#> 71.52947 94.59751 97.37680
#>
#> $`2D1`
#> 2D1.m.8 2D1.m.6 2D1.m.7 2D1.m.5 2D1.m.4 2D1.m.3 2D1.m.2 2D1.m.1
#> 0.00000 13.13829 13.13829 16.77185 17.73195 18.20947 18.71471 19.20363
#>
#> $`2D2`
#> 2D2.m.13 2D2.m.12 2D2.m.11 2D2.m.9 2D2.m.10 2D2.m.8 2D2.m.7 2D2.m.6
#> 0.000000 3.215434 10.137247 11.057585 11.516314 42.462800 46.604503 47.066011
#> 2D2.m.5 2D2.m.4 2D2.m.3 2D2.m.2 2D2.m.1
#> 49.363984 51.660473 59.519642 59.982755 60.441483
#>
#> $`3A`
#> 3A.m.37 3A.m.35 3A.m.36 3A.m.34 3A.m.33 3A.m.32
#> 0.0000000 0.4587285 0.4587285 1.8352229 2.2939514 4.5891402
#> 3A.m.31 3A.m.30 3A.m.29 3A.m.28 3A.m.27 3A.m.26
#> 5.5066743 7.4768940 15.9172288 26.6285944 38.3224121 44.3317651
#> 3A.m.25 3A.m.24 3A.m.23 3A.m.22 3A.m.21 3A.m.20
#> 50.7894517 56.7812731 57.2400015 63.6976881 64.6152223 65.5327565
#> 3A.m.19 3A.m.16 3A.m.17 3A.m.18 3A.m.15 3A.m.14
#> 68.7481909 82.8738429 83.7913771 84.2501056 85.6266000 86.0853285
#> 3A.m.13 3A.m.10 3A.m.9 3A.m.11 3A.m.12 3A.m.8
#> 86.5440569 90.6819179 92.0584123 93.4349067 95.7300955 126.0286198
#> 3A.m.7 3A.m.6 3A.m.5 3A.m.4 3A.m.3 3A.m.2
#> 126.9461540 133.4038406 134.3213748 137.9977120 144.9223833 145.3811118
#> 3A.m.1
#> 145.8398402
#>
#> $`3B`
#> 3B.m.30 3B.m.29 3B.m.28 3B.m.27 3B.m.26 3B.m.25 3B.m.24 3B.m.23
#> 0.00000 10.23223 22.39308 30.25542 34.39367 34.85278 38.99064 53.45212
#> 3B.m.22 3B.m.21 3B.m.20 3B.m.19 3B.m.17 3B.m.18 3B.m.16 3B.m.15
#> 56.35658 61.41969 66.48280 67.40033 68.31786 68.77659 69.23532 69.69405
#> 3B.m.14 3B.m.13 3B.m.11 3B.m.12 3B.m.10 3B.m.9 3B.m.8 3B.m.7
#> 73.83191 74.29064 74.74937 74.74937 75.20810 97.15983 98.07737 104.62584
#> 3B.m.6 3B.m.5 3B.m.4 3B.m.3 3B.m.2 3B.m.1
#> 129.29707 131.59226 132.05099 132.50972 133.42725 133.88598
#>
#> $`3D`
#> 3D.m.6 3D.m.5 3D.m.4 3D.m.3 3D.m.1 3D.m.2
#> 0.0000000 0.4587314 5.0589782 8.2768742 8.7379031 8.7379031
#>
#> $`4A.1`
#> 4A.m.9 4A.m.7 4A.m.8 4A.m.6 4A.m.5 4A.m.3 4A.m.4 4A.m.2
#> 0.000000 1.835687 1.835687 2.294415 2.753144 3.670678 4.129406 6.424595
#> 4A.m.1
#> 7.801089
#>
#> $`4A.2`
#> 4A.m.30 4A.m.29 4A.m.28 4A.m.27 4A.m.26 4A.m.25 4A.m.24 4A.m.23
#> 0.00000 6.92467 18.60024 26.93343 43.06735 44.44384 44.90257 45.82010
#> 4A.m.22 4A.m.21 4A.m.20 4A.m.19 4A.m.18 4A.m.17 4A.m.16 4A.m.15
#> 46.73764 47.19637 48.11390 51.79024 53.16673 53.62546 83.92398 84.38271
#> 4A.m.14 4A.m.13 4A.m.12 4A.m.11 4A.m.10
#> 86.67790 94.54023 94.99896 95.91650 98.21169
#>
#> $`4B`
#> 4B.m.32 4B.m.31 4B.m.30 4B.m.29 4B.m.28 4B.m.27 4B.m.26
#> 0.000000 8.333189 21.963866 22.881400 24.257894 29.784884 37.647217
#> 4B.m.25 4B.m.24 4B.m.23 4B.m.22 4B.m.21 4B.m.20 4B.m.19
#> 41.785078 42.243806 43.161340 50.086010 51.003544 52.380039 52.838767
#> 4B.m.18 4B.m.17 4B.m.16 4B.m.15 4B.m.14 4B.m.13 4B.m.12
#> 53.756301 56.051490 56.510218 58.345905 58.804634 59.263362 59.722091
#> 4B.m.11 4B.m.10 4B.m.9 4B.m.8 4B.m.7 4B.m.6 4B.m.5
#> 60.180819 60.639547 61.557082 62.015810 64.310999 78.436651 81.191729
#> 4B.m.4 4B.m.3 4B.m.2 4B.m.1
#> 83.946808 91.340123 91.799300 109.472825
#>
#> $`4D`
#> 4D.m.6 4D.m.5 4D.m.4 4D.m.3 4D.m.2 4D.m.1
#> 0.000000 4.600091 8.776795 10.651111 12.143891 13.255588
#>
#> $`5A`
#> 5A.m.54 5A.m.53 5A.m.52 5A.m.51 5A.m.50 5A.m.49
#> 0.0000000 0.4587285 0.9174569 1.8376979 19.5108820 38.7568771
#> 5A.m.48 5A.m.47 5A.m.46 5A.m.45 5A.m.44 5A.m.43
#> 39.2156055 41.0512923 49.8568071 50.3155356 50.7742640 51.2329925
#> 5A.m.42 5A.m.41 5A.m.40 5A.m.39 5A.m.38 5A.m.36
#> 51.6917210 53.0682154 58.1313220 58.5900505 60.4257372 61.8022316
#> 5A.m.37 5A.m.35 5A.m.34 5A.m.33 5A.m.32 5A.m.31
#> 61.8022316 62.2609601 63.1784942 66.3939287 69.1490072 70.0665414
#> 5A.m.30 5A.m.29 5A.m.28 5A.m.27 5A.m.26 5A.m.25
#> 70.5252698 72.3609565 73.7374510 74.1961794 76.0318662 79.7082016
#> 5A.m.24 5A.m.23 5A.m.22 5A.m.21 5A.m.20 5A.m.19
#> 80.1669301 86.1587514 87.0762856 100.7069618 105.7700684 106.2287969
#> 5A.m.18 5A.m.17 5A.m.16 5A.m.15 5A.m.14 5A.m.13
#> 106.6875254 108.0640198 109.4405142 117.7737037 119.6093904 123.7472514
#> 5A.m.12 5A.m.10 5A.m.11 5A.m.9 5A.m.8 5A.m.7
#> 128.3473425 130.6425312 131.1012597 160.1198614 166.1116828 171.1747894
#> 5A.m.6 5A.m.5 5A.m.4 5A.m.3 5A.m.2 5A.m.1
#> 172.0923235 172.5510520 173.0097805 174.8454672 175.3041956 181.7618822
#>
#> $`5B`
#> 5B.m.56 5B.m.55 5B.m.54 5B.m.53 5B.m.52 5B.m.51
#> 0.0000000 0.9175342 14.0558285 17.7321639 20.0273526 20.4860811
#> 5B.m.50 5B.m.49 5B.m.48 5B.m.47 5B.m.46 5B.m.45
#> 22.3217678 22.7804963 23.2392247 23.6979532 24.1566817 24.6154101
#> 5B.m.44 5B.m.43 5B.m.42 5B.m.41 5B.m.40 5B.m.39
#> 25.0741386 25.9916728 26.4504012 26.9091297 27.3678582 27.8265933
#> 5B.m.38 5B.m.37 5B.m.36 5B.m.35 5B.m.34 5B.m.33
#> 28.7680562 29.2508125 31.5461135 32.0048420 32.4635705 33.3811046
#> 5B.m.32 5B.m.31 5B.m.29 5B.m.30 5B.m.28 5B.m.27
#> 33.8398331 34.7573673 36.1338617 36.5925902 37.0513186 60.1193592
#> 5B.m.26 5B.m.25 5B.m.24 5B.m.23 5B.m.22 5B.m.21
#> 64.2572202 64.7159486 65.1746771 66.5511715 72.0781607 75.2935951
#> 5B.m.20 5B.m.19 5B.m.18 5B.m.17 5B.m.15 5B.m.16
#> 76.7000704 78.6053647 79.5624655 83.2388010 83.6975294 83.6975294
#> 5B.m.14 5B.m.13 5B.m.12 5B.m.11 5B.m.10 5B.m.9
#> 98.3208693 98.7795978 111.9178921 112.8354262 115.5905047 120.6536113
#> 5B.m.8 5B.m.7 5B.m.6 5B.m.5 5B.m.4 5B.m.3
#> 125.2537024 125.7124309 135.4673718 137.7625605 138.6800947 139.6333935
#> 5B.m.2 5B.m.1
#> 142.1178003 142.7883741
#>
#> $`5D`
#> 5D.m.6 5D.m.4 5D.m.5 5D.m.1 5D.m.2 5D.m.3
#> 0.0000000 0.4587285 0.4587285 17.1024336 17.5611621 18.0198906
#>
#> $`6A`
#> 6A.m.27 6A.m.26 6A.m.25 6A.m.24 6A.m.23 6A.m.22 6A.m.21
#> 0.0000000 0.4587285 3.2138070 3.6725354 4.5900696 29.3742386 37.2365718
#> 6A.m.20 6A.m.18 6A.m.19 6A.m.17 6A.m.16 6A.m.15 6A.m.14
#> 38.6130662 40.9082550 41.3669834 41.8257119 42.2844404 43.2019745 45.0376613
#> 6A.m.13 6A.m.12 6A.m.11 6A.m.10 6A.m.9 6A.m.8 6A.m.7
#> 51.9623308 56.1001918 63.9625251 65.3494460 74.1657062 74.6244347 79.6875413
#> 6A.m.6 6A.m.5 6A.m.4 6A.m.3 6A.m.2 6A.m.1
#> 91.3631163 93.1988030 95.0344897 97.3296785 98.2472126 98.7059411
#>
#> $`6B`
#> 6B.m.41 6B.m.40 6B.m.39 6B.m.38 6B.m.37 6B.m.36 6B.m.35
#> 0.000000 3.228588 4.666779 7.462087 9.716855 10.674985 11.133714
#> 6B.m.34 6B.m.33 6B.m.32 6B.m.31 6B.m.30 6B.m.29 6B.m.28
#> 13.428903 20.821759 23.152283 26.403125 43.559982 46.315061 46.773789
#> 6B.m.27 6B.m.26 6B.m.25 6B.m.24 6B.m.23 6B.m.22 6B.m.21
#> 47.232518 47.694728 55.553493 56.012221 58.767300 60.143794 60.602523
#> 6B.m.20 6B.m.19 6B.m.18 6B.m.16 6B.m.17 6B.m.15 6B.m.14
#> 62.438210 63.923978 64.732295 65.649829 66.108558 66.567286 67.943781
#> 6B.m.13 6B.m.12 6B.m.11 6B.m.10 6B.m.9 6B.m.8 6B.m.7
#> 68.402509 69.320043 73.457904 80.382574 80.841302 81.300031 101.078220
#> 6B.m.6 6B.m.5 6B.m.4 6B.m.2 6B.m.3 6B.m.1
#> 110.357621 110.816350 112.192844 114.488173 114.947042 115.406325
#>
#> $`6D`
#> 6D.m.15 6D.m.14 6D.m.13 6D.m.12 6D.m.11 6D.m.10 6D.m.9
#> 0.0000000 0.9225051 4.1379396 10.6171243 39.6108758 57.8493328 58.7668670
#> 6D.m.8 6D.m.7 6D.m.6 6D.m.5 6D.m.4 6D.m.2 6D.m.3
#> 59.2262509 69.4591643 69.9178927 70.8354269 71.2941554 71.7528838 71.7528838
#> 6D.m.1
#> 72.2116123
#>
#> $`7A`
#> 7A.m.32 7A.m.33 7A.m.31 7A.m.30 7A.m.29 7A.m.28 7A.m.27
#> 0.000000 0.000000 0.684333 4.106999 5.024533 5.488570 10.094015
#> 7A.m.26 7A.m.25 7A.m.24 7A.m.23 7A.m.22 7A.m.21 7A.m.20
#> 11.011549 18.873882 34.501225 36.796414 37.715916 47.472900 68.874166
#> 7A.m.19 7A.m.18 7A.m.17 7A.m.16 7A.m.15 7A.m.14 7A.m.13
#> 69.791700 70.709234 71.167963 72.085497 72.544226 73.920720 78.474431
#> 7A.m.12 7A.m.11 7A.m.10 7A.m.9 7A.m.8 7A.m.7 7A.m.6
#> 79.437975 80.814469 83.109658 84.027192 86.782271 87.240999 113.797115
#> 7A.m.5 7A.m.4 7A.m.3 7A.m.2 7A.m.1
#> 118.860222 127.193412 131.793503 133.796103 134.474614
#>
#> $`7B`
#> 7B.m.37 7B.m.36 7B.m.35 7B.m.34 7B.m.33 7B.m.31 7B.m.32 7B.m.30
#> 0.00000 23.63430 24.09303 27.76936 29.14586 30.06339 30.52212 36.04911
#> 7B.m.29 7B.m.28 7B.m.27 7B.m.26 7B.m.25 7B.m.24 7B.m.23 7B.m.21
#> 38.80419 39.72172 58.43965 59.35718 62.57262 65.32769 65.78642 69.00186
#> 7B.m.22 7B.m.20 7B.m.19 7B.m.17 7B.m.18 7B.m.16 7B.m.15 7B.m.14
#> 69.00186 69.91939 72.67447 74.96966 75.42839 75.88712 76.80465 77.26338
#> 7B.m.13 7B.m.12 7B.m.11 7B.m.10 7B.m.9 7B.m.8 7B.m.6 7B.m.7
#> 79.55857 80.47610 81.39364 81.85236 82.31109 83.22863 84.60512 85.36757
#> 7B.m.5 7B.m.4 7B.m.3 7B.m.2 7B.m.1
#> 86.91130 92.42609 92.88482 98.87664 108.15604
#>
#> $`7D`
#> 7D.m.4 7D.m.2 7D.m.3 7D.m.1
#> 0.000000 5.526989 5.526989 21.660902
#>
## one linkage group at a time (do not break established linkage groups)
test3 <- mstmap(mapDH, bychr = TRUE, dist.fun = "kosambi", p.value = 2,
trace = FALSE)
#> Number of linkage groups: 1
#> The size of the linkage groups are: 41
#> The number of bins in each linkage group: 41
#> Number of linkage groups: 1
#> The size of the linkage groups are: 5
#> The number of bins in each linkage group: 4
#> Number of linkage groups: 1
#> The size of the linkage groups are: 33
#> The number of bins in each linkage group: 33
#> Number of linkage groups: 1
#> The size of the linkage groups are: 10
#> The number of bins in each linkage group: 9
#> Number of linkage groups: 1
#> The size of the linkage groups are: 40
#> The number of bins in each linkage group: 40
#> Number of linkage groups: 1
#> The size of the linkage groups are: 35
#> The number of bins in each linkage group: 34
#> Number of linkage groups: 1
#> The size of the linkage groups are: 8
#> The number of bins in each linkage group: 7
#> Number of linkage groups: 1
#> The size of the linkage groups are: 13
#> The number of bins in each linkage group: 13
#> Number of linkage groups: 1
#> The size of the linkage groups are: 37
#> The number of bins in each linkage group: 36
#> Number of linkage groups: 1
#> The size of the linkage groups are: 30
#> The number of bins in each linkage group: 29
#> Number of linkage groups: 1
#> The size of the linkage groups are: 6
#> The number of bins in each linkage group: 5
#> Number of linkage groups: 1
#> The size of the linkage groups are: 30
#> The number of bins in each linkage group: 29
#> Number of linkage groups: 1
#> The size of the linkage groups are: 32
#> The number of bins in each linkage group: 32
#> Number of linkage groups: 1
#> The size of the linkage groups are: 6
#> The number of bins in each linkage group: 6
#> Number of linkage groups: 1
#> The size of the linkage groups are: 54
#> The number of bins in each linkage group: 53
#> Number of linkage groups: 1
#> The size of the linkage groups are: 56
#> The number of bins in each linkage group: 55
#> Number of linkage groups: 1
#> The size of the linkage groups are: 6
#> The number of bins in each linkage group: 5
#> Number of linkage groups: 1
#> The size of the linkage groups are: 27
#> The number of bins in each linkage group: 27
#> Number of linkage groups: 1
#> The size of the linkage groups are: 41
#> The number of bins in each linkage group: 41
#> Number of linkage groups: 1
#> The size of the linkage groups are: 15
#> The number of bins in each linkage group: 14
#> Number of linkage groups: 1
#> The size of the linkage groups are: 33
#> The number of bins in each linkage group: 32
#> Number of linkage groups: 1
#> The size of the linkage groups are: 37
#> The number of bins in each linkage group: 36
#> Number of linkage groups: 1
#> The size of the linkage groups are: 4
#> The number of bins in each linkage group: 3
pull.map(test3)
#> $`1A`
#> 1A.m.41 1A.m.40 1A.m.39 1A.m.38 1A.m.37 1A.m.36
#> 0.0000000 0.4587285 0.9174569 3.2126457 10.1373152 11.5138097
#> 1A.m.35 1A.m.34 1A.m.33 1A.m.32 1A.m.31 1A.m.30
#> 16.1139008 23.9762340 24.4349625 24.8936909 25.9826349 27.1876743
#> 1A.m.29 1A.m.28 1A.m.27 1A.m.26 1A.m.25 1A.m.24
#> 29.0233610 32.2387955 32.6975239 34.5332107 63.5518124 64.9283068
#> 1A.m.23 1A.m.22 1A.m.21 1A.m.20 1A.m.19 1A.m.18
#> 68.1437413 68.6024697 69.0611982 69.9787324 71.3552268 71.8139553
#> 1A.m.17 1A.m.16 1A.m.15 1A.m.13 1A.m.14 1A.m.12
#> 72.7314894 73.1902179 74.5667123 75.5029664 75.9804099 76.4391384
#> 1A.m.11 1A.m.10 1A.m.9 1A.m.8 1A.m.7 1A.m.6
#> 77.8156328 78.7331670 81.4882455 81.9469740 82.4057024 82.8644309
#> 1A.m.5 1A.m.4 1A.m.3 1A.m.2 1A.m.1
#> 83.3231594 84.6996538 99.8235155 102.5785940 103.9550885
#>
#> $`1B1`
#> 1B1.m.4 1B1.m.5 1B1.m.3 1B1.m.2 1B1.m.1
#> 0.000000 0.000000 4.137861 6.892939 7.810474
#>
#> $`1B2`
#> 1B2.m.33 1B2.m.32 1B2.m.31 1B2.m.30 1B2.m.29 1B2.m.28 1B2.m.27 1B2.m.26
#> 0.000000 9.279401 10.655895 11.573429 12.032158 13.867845 15.289476 16.711107
#> 1B2.m.25 1B2.m.24 1B2.m.23 1B2.m.22 1B2.m.21 1B2.m.20 1B2.m.19 1B2.m.18
#> 17.169836 18.546330 19.463864 20.851965 29.173232 31.008919 32.844606 36.520941
#> 1B2.m.17 1B2.m.16 1B2.m.15 1B2.m.14 1B2.m.13 1B2.m.12 1B2.m.11 1B2.m.10
#> 36.979670 38.356164 38.814893 40.650579 42.027074 42.944608 43.862142 44.320871
#> 1B2.m.9 1B2.m.8 1B2.m.7 1B2.m.6 1B2.m.5 1B2.m.4 1B2.m.3 1B2.m.2
#> 44.779599 46.156094 47.991780 48.450509 49.827003 51.203498 51.662226 59.995416
#> 1B2.m.1
#> 60.912950
#>
#> $`1D`
#> 1D.m.10 1D.m.9 1D.m.8 1D.m.7 1D.m.6 1D.m.5 1D.m.3 1D.m.4
#> 0.00000 22.50673 22.96620 23.88404 55.53218 59.75146 78.46976 78.46976
#> 1D.m.2 1D.m.1
#> 78.92881 81.22400
#>
#> $`2A`
#> 2A.m.40 2A.m.39 2A.m.38 2A.m.37 2A.m.36 2A.m.35 2A.m.34
#> 0.000000 2.654039 3.575343 4.953997 5.872637 7.249131 18.886363
#> 2A.m.33 2A.m.32 2A.m.31 2A.m.30 2A.m.29 2A.m.28 2A.m.26
#> 24.338629 24.797357 29.860464 30.319193 45.946535 46.885701 49.640780
#> 2A.m.27 2A.m.25 2A.m.24 2A.m.23 2A.m.22 2A.m.21 2A.m.20
#> 51.476466 52.394000 54.689189 57.904624 58.363352 58.822081 62.959942
#> 2A.m.19 2A.m.18 2A.m.17 2A.m.16 2A.m.15 2A.m.14 2A.m.13
#> 63.418670 76.067061 77.902748 80.657826 83.412910 83.886982 84.345711
#> 2A.m.12 2A.m.11 2A.m.10 2A.m.9 2A.m.8 2A.m.7 2A.m.6
#> 84.804439 85.263167 85.721896 101.855809 105.993670 106.452398 111.979387
#> 2A.m.5 2A.m.4 2A.m.3 2A.m.2 2A.m.1
#> 126.105039 127.940726 128.858260 138.613201 153.236541
#>
#> $`2B`
#> 2B.m.35 2B.m.33 2B.m.34 2B.m.31 2B.m.32 2B.m.30 2B.m.29 2B.m.28
#> 0.00000 16.64371 17.10243 18.47893 18.47893 18.93766 19.39638 19.85511
#> 2B.m.27 2B.m.26 2B.m.25 2B.m.24 2B.m.23 2B.m.22 2B.m.21 2B.m.20
#> 20.77265 21.69018 22.14891 23.98460 24.44333 25.81982 27.19631 27.65504
#> 2B.m.19 2B.m.18 2B.m.17 2B.m.16 2B.m.15 2B.m.14 2B.m.13 2B.m.12
#> 29.03154 29.94907 30.86661 31.32533 31.78406 32.24279 33.61929 35.45497
#> 2B.m.11 2B.m.10 2B.m.9 2B.m.8 2B.m.7 2B.m.6 2B.m.5 2B.m.4
#> 36.37251 45.17802 45.63675 46.09548 47.93116 56.26435 65.54376 71.07074
#> 2B.m.3 2B.m.2 2B.m.1
#> 71.52947 94.59751 97.37680
#>
#> $`2D1`
#> 2D1.m.8 2D1.m.6 2D1.m.7 2D1.m.5 2D1.m.4 2D1.m.3 2D1.m.2 2D1.m.1
#> 0.00000 13.13829 13.13829 16.77185 17.73195 18.20947 18.71471 19.20363
#>
#> $`2D2`
#> 2D2.m.13 2D2.m.12 2D2.m.11 2D2.m.9 2D2.m.10 2D2.m.8 2D2.m.7 2D2.m.6
#> 0.000000 3.215434 10.137247 11.057585 11.516314 42.462800 46.604503 47.066011
#> 2D2.m.5 2D2.m.4 2D2.m.3 2D2.m.2 2D2.m.1
#> 49.363984 51.660473 59.519642 59.982755 60.441483
#>
#> $`3A`
#> 3A.m.37 3A.m.35 3A.m.36 3A.m.34 3A.m.33 3A.m.32
#> 0.0000000 0.4587285 0.4587285 1.8352229 2.2939514 4.5891402
#> 3A.m.31 3A.m.30 3A.m.29 3A.m.28 3A.m.27 3A.m.26
#> 5.5066743 7.4768940 15.9172288 26.6285944 38.3224121 44.3317651
#> 3A.m.25 3A.m.24 3A.m.23 3A.m.22 3A.m.21 3A.m.20
#> 50.7894517 56.7812731 57.2400015 63.6976881 64.6152223 65.5327565
#> 3A.m.19 3A.m.18 3A.m.17 3A.m.16 3A.m.15 3A.m.14
#> 68.7481909 83.3715308 83.8302593 84.7477934 85.6653276 86.1240561
#> 3A.m.13 3A.m.10 3A.m.9 3A.m.11 3A.m.12 3A.m.8
#> 86.5827845 90.7206455 92.0971399 93.4736344 95.7688231 126.0673475
#> 3A.m.7 3A.m.6 3A.m.5 3A.m.4 3A.m.3 3A.m.2
#> 126.9848816 133.4425682 134.3601024 138.0364396 144.9611109 145.4198394
#> 3A.m.1
#> 145.8785678
#>
#> $`3B`
#> 3B.m.30 3B.m.29 3B.m.28 3B.m.27 3B.m.26 3B.m.25 3B.m.24 3B.m.23
#> 0.00000 10.23223 22.39308 30.25542 34.39367 34.85278 38.99064 53.45212
#> 3B.m.22 3B.m.21 3B.m.20 3B.m.19 3B.m.17 3B.m.18 3B.m.16 3B.m.15
#> 56.35658 61.41969 66.48280 67.40033 68.31786 68.77659 69.23532 69.69405
#> 3B.m.14 3B.m.13 3B.m.11 3B.m.12 3B.m.10 3B.m.9 3B.m.8 3B.m.7
#> 73.83191 74.29064 74.74937 74.74937 75.20810 97.15983 98.07737 104.62584
#> 3B.m.6 3B.m.5 3B.m.4 3B.m.3 3B.m.2 3B.m.1
#> 129.29707 131.59226 132.05099 132.50972 133.42725 133.88598
#>
#> $`3D`
#> 3D.m.6 3D.m.5 3D.m.4 3D.m.3 3D.m.1 3D.m.2
#> 0.0000000 0.4587314 5.0589782 8.2768742 8.7379031 8.7379031
#>
#> $`4A`
#> 4A.m.30 4A.m.29 4A.m.28 4A.m.27 4A.m.26 4A.m.25 4A.m.24 4A.m.23
#> 0.00000 6.92467 18.60024 26.93343 43.06735 44.44384 44.90257 45.82010
#> 4A.m.22 4A.m.21 4A.m.20 4A.m.19 4A.m.18 4A.m.17 4A.m.16 4A.m.15
#> 46.73764 47.19637 48.11390 51.79024 53.16673 53.62546 83.92398 84.38271
#> 4A.m.14 4A.m.13 4A.m.12 4A.m.11 4A.m.10 4A.m.9 4A.m.7 4A.m.8
#> 86.67790 94.54023 94.99896 95.91650 98.21169 140.42607 142.26175 142.26175
#> 4A.m.6 4A.m.5 4A.m.3 4A.m.4 4A.m.2 4A.m.1
#> 142.72048 143.17921 144.09674 144.55547 146.85066 148.22716
#>
#> $`4B`
#> 4B.m.32 4B.m.31 4B.m.30 4B.m.29 4B.m.28 4B.m.27 4B.m.26
#> 0.000000 8.333189 21.963866 22.881400 24.257894 29.784884 37.647217
#> 4B.m.25 4B.m.24 4B.m.23 4B.m.22 4B.m.21 4B.m.20 4B.m.19
#> 41.785078 42.243806 43.161340 50.086010 51.003544 52.380039 52.838767
#> 4B.m.18 4B.m.17 4B.m.16 4B.m.15 4B.m.14 4B.m.13 4B.m.12
#> 53.756301 56.051490 56.510218 58.345905 58.804634 59.263362 59.722091
#> 4B.m.11 4B.m.10 4B.m.9 4B.m.8 4B.m.7 4B.m.6 4B.m.5
#> 60.180819 60.639547 61.557082 62.015810 64.310999 78.436651 81.191729
#> 4B.m.4 4B.m.3 4B.m.2 4B.m.1
#> 83.946808 91.340123 91.799300 109.472825
#>
#> $`4D`
#> 4D.m.6 4D.m.5 4D.m.4 4D.m.3 4D.m.2 4D.m.1
#> 0.000000 4.600091 8.776795 10.651111 12.143891 13.255588
#>
#> $`5A`
#> 5A.m.54 5A.m.53 5A.m.52 5A.m.51 5A.m.50 5A.m.49
#> 0.0000000 0.4587285 0.9174569 1.8376979 19.5108820 38.7568771
#> 5A.m.48 5A.m.47 5A.m.46 5A.m.45 5A.m.44 5A.m.43
#> 39.2156055 41.0512923 49.8568071 50.3155356 50.7742640 51.2329925
#> 5A.m.42 5A.m.41 5A.m.40 5A.m.39 5A.m.38 5A.m.36
#> 51.6917210 53.0682154 58.1313220 58.5900505 60.4257372 61.8022316
#> 5A.m.37 5A.m.35 5A.m.34 5A.m.33 5A.m.32 5A.m.31
#> 61.8022316 62.2609601 63.1784942 66.3939287 69.1490072 70.0665414
#> 5A.m.30 5A.m.29 5A.m.28 5A.m.27 5A.m.26 5A.m.25
#> 70.5252698 72.3609565 73.7374510 74.1961794 76.0318662 79.7082016
#> 5A.m.24 5A.m.23 5A.m.22 5A.m.21 5A.m.20 5A.m.19
#> 80.1669301 86.1587514 87.0762856 100.7069618 105.7700684 106.2287969
#> 5A.m.18 5A.m.17 5A.m.16 5A.m.15 5A.m.14 5A.m.13
#> 106.6875254 108.0640198 109.4405142 117.7737037 119.6093904 123.7472514
#> 5A.m.12 5A.m.10 5A.m.11 5A.m.9 5A.m.8 5A.m.7
#> 128.3473425 130.6425312 131.1012597 160.1198614 166.1116828 171.1747894
#> 5A.m.6 5A.m.5 5A.m.4 5A.m.3 5A.m.2 5A.m.1
#> 172.0923235 172.5510520 173.0097805 174.8454672 175.3041956 181.7618822
#>
#> $`5B`
#> 5B.m.56 5B.m.55 5B.m.54 5B.m.53 5B.m.52 5B.m.51
#> 0.0000000 0.9175342 14.0558285 17.7321639 20.0273526 20.4860811
#> 5B.m.50 5B.m.49 5B.m.48 5B.m.47 5B.m.46 5B.m.45
#> 22.3217678 22.7804963 23.2392247 23.6979532 24.1566817 24.6154101
#> 5B.m.44 5B.m.43 5B.m.42 5B.m.41 5B.m.40 5B.m.39
#> 25.0741386 25.9916728 26.4504012 26.9091297 27.3678582 27.8265933
#> 5B.m.38 5B.m.37 5B.m.36 5B.m.35 5B.m.34 5B.m.33
#> 28.7680562 29.2508125 31.5461135 32.0048420 32.4635705 33.3811046
#> 5B.m.32 5B.m.31 5B.m.29 5B.m.30 5B.m.28 5B.m.27
#> 33.8398331 34.7573673 36.1338617 36.5925902 37.0513186 60.1193592
#> 5B.m.26 5B.m.25 5B.m.24 5B.m.23 5B.m.22 5B.m.21
#> 64.2572202 64.7159486 65.1746771 66.5511715 72.0781607 75.2935951
#> 5B.m.20 5B.m.19 5B.m.18 5B.m.17 5B.m.15 5B.m.16
#> 76.7000704 78.6053647 79.5624655 83.2388010 83.6975294 83.6975294
#> 5B.m.14 5B.m.13 5B.m.12 5B.m.11 5B.m.10 5B.m.9
#> 98.3208693 98.7795978 111.9178921 112.8354262 115.5905047 120.6536113
#> 5B.m.8 5B.m.7 5B.m.6 5B.m.5 5B.m.4 5B.m.3
#> 125.2537024 125.7124309 135.4673718 137.7625605 138.6800947 139.6333935
#> 5B.m.2 5B.m.1
#> 142.1178003 142.7883741
#>
#> $`5D`
#> 5D.m.6 5D.m.4 5D.m.5 5D.m.1 5D.m.2 5D.m.3
#> 0.0000000 0.4587285 0.4587285 17.1024336 17.5611621 18.0198906
#>
#> $`6A`
#> 6A.m.27 6A.m.26 6A.m.25 6A.m.24 6A.m.23 6A.m.22 6A.m.21
#> 0.0000000 0.4587285 3.2138070 3.6725354 4.5900696 29.3742386 37.2365718
#> 6A.m.20 6A.m.18 6A.m.19 6A.m.17 6A.m.16 6A.m.15 6A.m.14
#> 38.6130662 40.9082550 41.3669834 41.8257119 42.2844404 43.2019745 45.0376613
#> 6A.m.13 6A.m.12 6A.m.11 6A.m.10 6A.m.9 6A.m.8 6A.m.7
#> 51.9623308 56.1001918 63.9625251 65.3494460 74.1657062 74.6244347 79.6875413
#> 6A.m.6 6A.m.5 6A.m.4 6A.m.3 6A.m.2 6A.m.1
#> 91.3631163 93.1988030 95.0344897 97.3296785 98.2472126 98.7059411
#>
#> $`6B`
#> 6B.m.41 6B.m.40 6B.m.39 6B.m.38 6B.m.37 6B.m.36 6B.m.35
#> 0.000000 3.228588 4.666779 7.462087 9.716855 10.674985 11.133714
#> 6B.m.34 6B.m.33 6B.m.32 6B.m.31 6B.m.30 6B.m.29 6B.m.28
#> 13.428903 20.821759 23.152283 26.403125 43.559982 46.315061 46.773789
#> 6B.m.27 6B.m.26 6B.m.25 6B.m.24 6B.m.23 6B.m.22 6B.m.21
#> 47.232518 47.694728 55.553493 56.012221 58.767300 60.143794 60.602523
#> 6B.m.20 6B.m.19 6B.m.18 6B.m.16 6B.m.17 6B.m.15 6B.m.14
#> 62.438210 63.923978 64.732295 65.649829 66.108558 66.567286 67.943781
#> 6B.m.13 6B.m.12 6B.m.11 6B.m.10 6B.m.9 6B.m.8 6B.m.7
#> 68.402509 69.320043 73.457904 80.382574 80.841302 81.300031 101.078220
#> 6B.m.6 6B.m.5 6B.m.4 6B.m.2 6B.m.3 6B.m.1
#> 110.357621 110.816350 112.192844 114.488173 114.947042 115.406325
#>
#> $`6D`
#> 6D.m.15 6D.m.14 6D.m.13 6D.m.12 6D.m.11 6D.m.10 6D.m.9
#> 0.0000000 0.9225051 4.1379396 10.6171243 39.6108758 57.8493328 58.7668670
#> 6D.m.8 6D.m.7 6D.m.6 6D.m.5 6D.m.4 6D.m.2 6D.m.3
#> 59.2262509 69.4591643 69.9178927 70.8354269 71.2941554 71.7528838 71.7528838
#> 6D.m.1
#> 72.2116123
#>
#> $`7A`
#> 7A.m.32 7A.m.33 7A.m.31 7A.m.30 7A.m.29 7A.m.28 7A.m.27
#> 0.000000 0.000000 0.684333 4.106999 5.024533 5.488570 10.094015
#> 7A.m.26 7A.m.25 7A.m.24 7A.m.23 7A.m.22 7A.m.21 7A.m.20
#> 11.011549 18.873882 34.501225 36.796414 37.715916 47.472900 68.874166
#> 7A.m.19 7A.m.18 7A.m.17 7A.m.16 7A.m.15 7A.m.14 7A.m.13
#> 69.791700 70.709234 71.167963 72.085497 72.544226 73.920720 78.474431
#> 7A.m.12 7A.m.11 7A.m.10 7A.m.9 7A.m.8 7A.m.7 7A.m.6
#> 79.437975 80.814469 83.109658 84.027192 86.782271 87.240999 113.797115
#> 7A.m.5 7A.m.4 7A.m.3 7A.m.2 7A.m.1
#> 118.860222 127.193412 131.793503 133.796103 134.474614
#>
#> $`7B`
#> 7B.m.37 7B.m.36 7B.m.35 7B.m.34 7B.m.33 7B.m.31 7B.m.32 7B.m.30
#> 0.00000 23.63430 24.09303 27.76936 29.14586 30.06339 30.52212 36.04911
#> 7B.m.29 7B.m.28 7B.m.27 7B.m.26 7B.m.25 7B.m.24 7B.m.23 7B.m.21
#> 38.80419 39.72172 58.43965 59.35718 62.57262 65.32769 65.78642 69.00186
#> 7B.m.22 7B.m.20 7B.m.19 7B.m.17 7B.m.18 7B.m.16 7B.m.15 7B.m.14
#> 69.00186 69.91939 72.67447 74.96966 75.42839 75.88712 76.80465 77.26338
#> 7B.m.13 7B.m.12 7B.m.11 7B.m.10 7B.m.9 7B.m.8 7B.m.6 7B.m.7
#> 79.55857 80.47610 81.39364 81.85236 82.31109 83.22863 84.60512 85.36757
#> 7B.m.5 7B.m.4 7B.m.3 7B.m.2 7B.m.1
#> 86.91130 92.42609 92.88482 98.87664 108.15604
#>
#> $`7D`
#> 7D.m.4 7D.m.2 7D.m.3 7D.m.1
#> 0.000000 5.526989 5.526989 21.660902
#>
## impute before clustering and detect genotyping errors, pipe output to
## file
test4 <- mstmap(mapDH, bychr = FALSE, dist.fun = "kosambi",
trace = TRUE, mvest.bc = TRUE, detectBadData = TRUE)
pull.map(test4)
#> $L.1
#> 1A.m.41 1A.m.40 1A.m.39 1A.m.38 1A.m.36 1A.m.37 1A.m.35
#> 0.0000000 0.0000000 0.0000000 0.4707376 9.9782181 10.3684549 15.1908593
#> 1A.m.34 1A.m.33 1A.m.32 1A.m.31 1A.m.30 1A.m.29 1A.m.27
#> 22.5837154 22.5837154 23.0424439 23.0424439 23.0424439 23.5243019 28.5991334
#> 1A.m.28 1A.m.26 1A.m.25 1A.m.24 1A.m.23 1A.m.22 1A.m.21
#> 28.5991334 29.0002364 62.6659641 62.6659641 66.3422926 66.3422926 66.3422926
#> 1A.m.20 1A.m.19 1A.m.18 1A.m.17 1A.m.16 1A.m.15 1A.m.13
#> 67.7166334 69.5510783 69.5510783 70.4686124 70.4686124 72.7611026 72.7611026
#> 1A.m.14 1A.m.12 1A.m.11 1A.m.10 1A.m.9 1A.m.8 1A.m.7
#> 72.7611026 72.7611026 74.5965083 74.5965083 78.7322150 78.7322150 79.1909435
#> 1A.m.6 1A.m.5 1A.m.4 1A.m.3 1A.m.1 1A.m.2
#> 79.6496719 79.6496719 80.1096325 99.8815346 99.8815346 99.8815346
#>
#> $L.10
#> 3B.m.30 3B.m.29 3B.m.28 3B.m.27 3B.m.25 3B.m.26 3B.m.24 3B.m.22
#> 0.00000 0.00000 19.45442 22.91261 23.38085 23.38085 23.81417 45.76099
#> 3B.m.23 3B.m.21 3B.m.20 3B.m.19 3B.m.18 3B.m.17 3B.m.16 3B.m.15
#> 45.76099 50.36004 56.35033 56.80465 56.80465 56.80465 57.26338 57.26338
#> 3B.m.14 3B.m.11 3B.m.12 3B.m.10 3B.m.13 3B.m.8 3B.m.9 3B.m.7
#> 62.32647 62.78521 62.78521 62.78521 63.24394 85.23370 85.23370 86.15508
#> 3B.m.6 3B.m.5 3B.m.4 3B.m.3 3B.m.1 3B.m.2
#> 121.91725 122.37604 122.37604 122.37604 123.74933 123.74933
#>
#> $L.11
#> 3D.m.5 3D.m.6 3D.m.4 3D.m.3 3D.m.1 3D.m.2
#> 0.000000 0.000000 4.579348 7.794824 7.794824 7.794824
#>
#> $L.12
#> 4A.m.7 4A.m.8 4A.m.9 4A.m.6 4A.m.5 4A.m.4 4A.m.3 4A.m.2
#> 0.0000000 0.0000000 0.4295604 0.4295604 0.8882888 1.3470173 1.8057458 4.4953910
#> 4A.m.1
#> 4.6067660
#>
#> $L.13
#> 4A.m.29 4A.m.30 4A.m.28 4A.m.27 4A.m.26 4A.m.25 4A.m.24 4A.m.23
#> 0.00000 0.00000 10.74765 17.68147 33.81539 34.27024 34.27024 35.18777
#> 4A.m.21 4A.m.22 4A.m.20 4A.m.19 4A.m.18 4A.m.17 4A.m.15 4A.m.16
#> 36.23123 36.42670 36.73804 41.79060 41.79060 41.79060 72.78102 72.78102
#> 4A.m.14 4A.m.12 4A.m.13 4A.m.11 4A.m.10
#> 73.22419 83.62258 83.85181 84.19123 84.99929
#>
#> $L.14
#> 4B.m.32 4B.m.31 4B.m.30 4B.m.29 4B.m.28 4B.m.27 4B.m.26 4B.m.24
#> 0.00000 0.00000 13.13829 13.13829 13.13829 19.59578 30.30334 30.47647
#> 4B.m.25 4B.m.23 4B.m.22 4B.m.21 4B.m.19 4B.m.20 4B.m.18 4B.m.16
#> 30.70000 30.95475 39.75684 39.75684 41.29357 41.51076 41.81285 45.09235
#> 4B.m.17 4B.m.15 4B.m.14 4B.m.13 4B.m.12 4B.m.11 4B.m.10 4B.m.9
#> 45.24587 47.90184 47.90184 48.36057 48.81930 49.27803 49.27803 50.64872
#> 4B.m.8 4B.m.7 4B.m.6 4B.m.5 4B.m.4 4B.m.2 4B.m.3 4B.m.1
#> 50.64872 51.10700 69.82403 69.82403 69.82403 80.04500 80.04500 80.50391
#>
#> $L.15
#> 4D.m.6 4D.m.5 4D.m.4 4D.m.3 4D.m.2 4D.m.1
#> 0.000000 0.000000 5.989233 5.989233 7.501043 7.694335
#>
#> $L.16
#> 5A.m.54 5A.m.53 5A.m.52 5A.m.51 5A.m.50 5A.m.48 5A.m.49
#> 0.000000 0.000000 0.000000 0.450987 17.094394 35.352126 35.455101
#> 5A.m.47 5A.m.46 5A.m.45 5A.m.44 5A.m.43 5A.m.42 5A.m.41
#> 35.868137 47.043409 47.043409 47.502137 47.960866 47.960866 48.428013
#> 5A.m.39 5A.m.40 5A.m.38 5A.m.36 5A.m.37 5A.m.35 5A.m.34
#> 54.761737 54.932223 58.026116 58.490930 58.490930 58.490930 58.926609
#> 5A.m.33 5A.m.32 5A.m.31 5A.m.30 5A.m.29 5A.m.28 5A.m.27
#> 63.062247 66.737951 66.737951 66.737951 68.995831 69.913366 69.913366
#> 5A.m.26 5A.m.24 5A.m.25 5A.m.23 5A.m.22 5A.m.21 5A.m.20
#> 69.913366 75.443389 75.443389 81.900131 81.900131 102.206118 102.664841
#> 5A.m.19 5A.m.18 5A.m.17 5A.m.16 5A.m.14 5A.m.15 5A.m.13
#> 102.664841 102.664841 104.500194 104.500194 114.778088 115.519843 120.975899
#> 5A.m.12 5A.m.11 5A.m.10 5A.m.9 5A.m.8 5A.m.7 5A.m.6
#> 127.430562 127.430562 127.430562 163.995004 168.813300 169.951103 170.420974
#> 5A.m.5 5A.m.4 5A.m.3 5A.m.2 5A.m.1
#> 170.420974 170.420974 172.716777 172.716777 172.716777
#>
#> $L.17
#> 5B.m.55 5B.m.56 5B.m.54 5B.m.53 5B.m.52 5B.m.51 5B.m.50 5B.m.49
#> 0.00000 0.00000 18.15690 20.41107 20.54125 20.68951 23.34758 23.34758
#> 5B.m.48 5B.m.47 5B.m.46 5B.m.45 5B.m.44 5B.m.43 5B.m.42 5B.m.41
#> 23.80631 24.26504 24.72377 25.18250 25.18250 27.00921 27.00921 27.46794
#> 5B.m.40 5B.m.39 5B.m.38 5B.m.37 5B.m.36 5B.m.35 5B.m.34 5B.m.33
#> 27.92667 27.92667 29.30019 29.30019 32.51499 32.51499 32.97372 33.89125
#> 5B.m.32 5B.m.31 5B.m.30 5B.m.29 5B.m.28 5B.m.27 5B.m.26 5B.m.25
#> 33.89125 35.26078 36.17831 36.17831 36.17831 65.19352 65.65469 65.65469
#> 5B.m.24 5B.m.23 5B.m.22 5B.m.21 5B.m.20 5B.m.19 5B.m.18 5B.m.17
#> 65.65469 66.11708 73.03634 77.63305 77.63305 78.55295 78.55295 82.69080
#> 5B.m.15 5B.m.16 5B.m.13 5B.m.14 5B.m.11 5B.m.12 5B.m.10 5B.m.9
#> 82.69080 82.69080 97.31725 97.31725 111.14453 111.44923 112.75248 120.01552
#> 5B.m.7 5B.m.8 5B.m.6 5B.m.5 5B.m.4 5B.m.3 5B.m.2 5B.m.1
#> 124.62152 124.62152 136.27801 137.19685 137.19685 137.19685 140.61763 140.87587
#>
#> $L.18
#> 5D.m.6 5D.m.4 5D.m.5 5D.m.3 5D.m.2 5D.m.1
#> 0.00000 0.00000 0.00000 17.15686 17.15686 17.15686
#>
#> $L.19
#> 6A.m.26 6A.m.27 6A.m.24 6A.m.25 6A.m.23 6A.m.21 6A.m.22 6A.m.20
#> 0.000000 0.000000 3.345266 3.574243 3.805474 38.894390 38.894390 38.894390
#> 6A.m.19 6A.m.18 6A.m.17 6A.m.16 6A.m.15 6A.m.14 6A.m.13 6A.m.12
#> 40.730077 40.730077 41.188805 41.188805 41.749814 42.553294 51.358808 51.358808
#> 6A.m.10 6A.m.11 6A.m.8 6A.m.9 6A.m.7 6A.m.6 6A.m.5 6A.m.4
#> 61.546796 61.546796 68.948092 68.948092 69.453075 86.547562 86.547562 88.383248
#> 6A.m.3 6A.m.1 6A.m.2
#> 91.597386 91.597386 91.597386
#>
#> $L.2
#> 1B1.m.4 1B1.m.5 1B1.m.3 1B1.m.1 1B1.m.2
#> 0.000000 0.000000 4.137861 6.892939 6.892939
#>
#> $L.20
#> 6B.m.39 6B.m.40 6B.m.41 6B.m.37 6B.m.35 6B.m.36
#> 0.0000000 0.4515493 1.5257130 2.9038432 2.9038432 3.0068008
#> 6B.m.34 6B.m.38 6B.m.33 6B.m.31 6B.m.32 6B.m.30
#> 3.4044709 3.8879560 15.5711836 15.5711836 15.5711836 39.7776891
#> 6B.m.29 6B.m.28 6B.m.27 6B.m.26 6B.m.24 6B.m.25
#> 40.2362277 40.2362277 40.6949562 40.6949562 49.0971561 49.2125657
#> 6B.m.23 6B.m.22 6B.m.21 6B.m.20 6B.m.17 6B.m.19
#> 53.2816940 53.2816940 53.2816940 54.1992282 54.1992282 54.1992282
#> 6B.m.18 6B.m.16 6B.m.15 6B.m.13 6B.m.14 6B.m.12
#> 54.1992282 54.1992282 54.1992282 56.1629237 56.3624912 56.6866103
#> 6B.m.11 6B.m.10 6B.m.9 6B.m.8 6B.m.7 6B.m.5
#> 57.5766755 68.2880410 68.2880410 68.2880410 100.5596715 100.6728366
#> 6B.m.6 6B.m.4 6B.m.2 6B.m.3 6B.m.1
#> 100.8327267 102.5641833 104.3998701 104.3998701 104.3998701
#>
#> $L.21
#> 6D.m.14 6D.m.15 6D.m.13 6D.m.12 6D.m.11 6D.m.10 6D.m.9
#> 0.0000000 0.2648916 1.2563401 3.8123288 60.9675620 62.3507222 62.3507222
#> 6D.m.8 6D.m.7 6D.m.6 6D.m.5 6D.m.4 6D.m.1 6D.m.2
#> 62.3507222 73.5420794 73.5420794 74.0008078 74.0008078 74.4595363 74.4595363
#> 6D.m.3
#> 74.4595363
#>
#> $L.22
#> 7A.m.32 7A.m.33 7A.m.31 7A.m.30 7A.m.29 7A.m.28
#> 0.0000000 0.0000000 0.2304851 5.0439148 5.0439148 5.0439148
#> 7A.m.26 7A.m.27 7A.m.25 7A.m.24 7A.m.23 7A.m.22
#> 10.1179695 10.1179695 11.0321717 36.3762789 36.3762789 36.3762789
#> 7A.m.21 7A.m.20 7A.m.19 7A.m.18 7A.m.17 7A.m.16
#> 46.5955942 68.5473322 68.9993429 68.9993429 68.9993429 69.9168771
#> 7A.m.15 7A.m.14 7A.m.13 7A.m.12 7A.m.11 7A.m.10
#> 69.9168771 70.3797639 77.2967170 77.2967170 78.6732115 80.0497109
#> 7A.m.9 7A.m.8 7A.m.7 7A.m.6 7A.m.5 7A.m.4
#> 80.0497109 82.8047894 82.8047894 117.1717214 117.1717214 130.1204011
#> 7A.m.3 7A.m.2 7A.m.1
#> 132.1081693 132.2517429 132.4461639
#>
#> $L.23
#> 7B.m.36 7B.m.35 7B.m.37 7B.m.34 7B.m.33 7B.m.32 7B.m.31
#> 0.0000000 0.0000000 0.5569769 5.5455454 6.0212678 6.0212678 6.0212678
#> 7B.m.30 7B.m.29 7B.m.28 7B.m.26 7B.m.27 7B.m.25 7B.m.23
#> 11.5482570 14.3033355 14.3033355 34.0815252 34.4196216 38.3284694 41.1219132
#> 7B.m.24 7B.m.21 7B.m.22 7B.m.20 7B.m.19 7B.m.18 7B.m.17
#> 41.1219132 44.7595183 44.7595183 44.7595183 50.2699348 50.2699348 50.2699348
#> 7B.m.16 7B.m.15 7B.m.14 7B.m.13 7B.m.12 7B.m.11 7B.m.10
#> 50.2699348 51.6428632 51.6428632 55.3154478 55.3154478 56.6890272 56.6890272
#> 7B.m.9 7B.m.8 7B.m.7 7B.m.6 7B.m.5 7B.m.3 7B.m.4
#> 56.6890272 58.0595921 58.6967364 58.9806390 59.4429459 66.3725092 66.3725092
#> 7B.m.2 7B.m.1
#> 66.9559701 73.2819914
#>
#> $L.24
#> 7D.m.4 7D.m.2 7D.m.3 7D.m.1
#> 0 0 0 0
#>
#> $L.3
#> 1B2.m.33 1B2.m.32 1B2.m.31 1B2.m.30 1B2.m.29 1B2.m.28 1B2.m.27
#> 0.0000000 0.4587285 1.3029093 1.4289748 1.4289748 4.1210023 4.1210023
#> 1B2.m.26 1B2.m.25 1B2.m.24 1B2.m.23 1B2.m.22 1B2.m.21 1B2.m.20
#> 4.5826840 4.5826840 6.4173981 6.4173981 7.2897289 16.0941551 16.0941551
#> 1B2.m.19 1B2.m.17 1B2.m.18 1B2.m.16 1B2.m.15 1B2.m.14 1B2.m.13
#> 17.9298418 21.7593855 21.9655462 24.0996427 24.0996427 24.5583711 24.5583711
#> 1B2.m.12 1B2.m.11 1B2.m.10 1B2.m.9 1B2.m.8 1B2.m.6 1B2.m.7
#> 25.4759053 26.8476927 26.8476927 26.8476927 28.6831147 30.6073916 30.7516149
#> 1B2.m.5 1B2.m.4 1B2.m.3 1B2.m.1 1B2.m.2
#> 32.4964175 33.8729120 33.8729120 42.6784268 42.6784268
#>
#> $L.4
#> 1D.m.8 1D.m.9 1D.m.7 1D.m.10 1D.m.5 1D.m.6 1D.m.3
#> 0.0000000 0.2325776 0.4467646 4.8951007 33.5565057 35.1842316 57.4356253
#> 1D.m.4 1D.m.2 1D.m.1
#> 57.4356253 57.4356253 57.8942535
#>
#> $L.5
#> 2A.m.39 2A.m.40 2A.m.38 2A.m.37 2A.m.36 2A.m.35 2A.m.34
#> 0.000000 0.000000 0.000000 1.376916 1.836066 1.836066 19.441233
#> 2A.m.32 2A.m.33 2A.m.30 2A.m.31 2A.m.29 2A.m.28 2A.m.26
#> 20.108910 20.108910 26.073209 26.073209 41.716710 41.716710 42.634244
#> 2A.m.27 2A.m.25 2A.m.24 2A.m.23 2A.m.22 2A.m.21 2A.m.20
#> 42.634244 42.634244 45.848455 49.524783 49.524783 49.524783 54.124872
#> 2A.m.19 2A.m.18 2A.m.17 2A.m.16 2A.m.15 2A.m.14 2A.m.13
#> 54.124872 69.248733 69.707163 69.707163 69.707163 69.707163 70.165891
#> 2A.m.12 2A.m.11 2A.m.10 2A.m.9 2A.m.7 2A.m.8 2A.m.6
#> 70.624619 71.083348 71.083348 92.475166 92.475166 92.475166 92.961913
#> 2A.m.4 2A.m.5 2A.m.3 2A.m.2 2A.m.1
#> 114.318005 114.318005 114.318005 116.545148 123.771568
#>
#> $L.6
#> 2B.m.35 2B.m.34 2B.m.33 2B.m.31 2B.m.32 2B.m.30 2B.m.29
#> 0.0000000 0.4695553 0.4695553 1.8460497 1.8460497 2.3047782 2.7635067
#> 2B.m.28 2B.m.27 2B.m.26 2B.m.25 2B.m.23 2B.m.24 2B.m.22
#> 2.7635067 4.1339848 4.5927133 4.5927133 6.5117357 6.6491104 8.3996927
#> 2B.m.20 2B.m.21 2B.m.19 2B.m.18 2B.m.17 2B.m.16 2B.m.15
#> 9.8735883 10.0284758 11.7640394 12.6815736 14.0546235 14.0546235 14.5133520
#> 2B.m.14 2B.m.13 2B.m.12 2B.m.11 2B.m.10 2B.m.9 2B.m.8
#> 14.5133520 16.3486657 18.1843524 18.1843524 28.4165824 28.4165824 28.4165824
#> 2B.m.7 2B.m.6 2B.m.5 2B.m.3 2B.m.4 2B.m.1 2B.m.2
#> 28.8765099 38.1543503 46.9615968 52.0276238 52.0276238 75.6110716 75.7219819
#>
#> $L.7
#> 2D1.m.6 2D1.m.7 2D1.m.8 2D1.m.5 2D1.m.4 2D1.m.3 2D1.m.1 2D1.m.2
#> 0.0000000 0.0000000 0.4587285 4.5664939 5.0280757 5.0280757 5.4903266 5.4903266
#>
#> $L.8
#> 2D2.m.13 2D2.m.12 2D2.m.10 2D2.m.9 2D2.m.11 2D2.m.8 2D2.m.7 2D2.m.6
#> 0.000000 0.000000 6.457687 6.457687 6.457687 36.756312 36.756312 36.756312
#> 2D2.m.5 2D2.m.4 2D2.m.3 2D2.m.2 2D2.m.1
#> 38.559460 38.559460 48.313484 48.313484 48.313484
#>
#> $L.9
#> 3A.m.37 3A.m.35 3A.m.36 3A.m.33 3A.m.34 3A.m.32 3A.m.31
#> 0.000000 0.000000 0.000000 1.414973 1.414973 4.131151 4.131151
#> 3A.m.30 3A.m.29 3A.m.28 3A.m.27 3A.m.26 3A.m.25 3A.m.23
#> 5.177161 7.525530 25.614865 43.265529 43.265529 49.257350 55.261756
#> 3A.m.24 3A.m.22 3A.m.21 3A.m.20 3A.m.19 3A.m.16 3A.m.17
#> 55.261756 62.641921 62.641921 62.641921 63.103611 80.773459 81.232188
#> 3A.m.18 3A.m.15 3A.m.14 3A.m.13 3A.m.11 3A.m.10 3A.m.9
#> 81.232188 83.063587 83.063587 83.063587 87.196692 87.196692 87.196692
#> 3A.m.12 3A.m.7 3A.m.8 3A.m.5 3A.m.6 3A.m.4 3A.m.3
#> 88.114226 121.204365 121.349262 128.775291 128.973077 133.458782 140.851640
#> 3A.m.2 3A.m.1
#> 140.851640 140.851640
#>
unlink("MSToutput.txt")