ASMap provides two construction functions, both methods of the
mstmap() generic. They differ only in the object they
accept: a data frame of marker scores, or an R/qtl cross
object. Both expose the full set of MSTmap parameters documented at http://alumni.cs.ucr.edu/~yonghui/mstmap.html.
The algorithm underlying them is described in How the MSTmap algorithm works, and the
practical behaviour of the mvest.bc and
detectBadData arguments in Notes on the MSTmap algorithm.
Example data
The package supplies five data sets, described in full on their
reference pages. The datasets are not lazy-loaded and require an
explicit data() call.
| Data set | Form | Individuals | Markers | Description |
|---|---|---|---|---|
mapDH |
cross | 218 | 599 | Constructed doubled haploid map, 23 linkage groups, containing a few co-located and distorted markers |
mapDHf |
data frame | 218 | 599 | Unconstructed form of mapDH, with the marker rows
randomised |
mapBCu |
cross | 326 | 3023 | Unconstructed backcross marker set |
mapBC |
cross | 300 | 3019 | Constructed form of mapBCu
|
mapF2 |
cross | 250 | 700 | Simulated selfed F2 map, 7 linkage groups |
Construction from a data frame
mstmap.data.frame()
accepts a data frame of marker scores. Its required layout derives from
the marker file used by the standalone MSTmap software: markers
in rows and genotypes in columns, with marker names in the
rownames and genotype names in the names.
Every column must be of class "character" rather than a
factor, which is most easily ensured through the
stringsAsFactors = FALSE argument of any
data.frame method. Spaces in marker or genotype names
should be avoided; where found they are replaced by a hyphen.
The allelic coding is strict, and depends on the population type
given to pop.type.
pop.type |
Population | Allele coding |
|---|---|---|
"BC" |
Backcross |
"A" or "a", and "B" or
"b"
|
"DH" |
Doubled haploid |
"A" or "a", and "B" or
"b"
|
"ARIL" |
Advanced recombinant inbred |
"A" or "a", and "B" or
"b"; heterozygotes assumed already set to missing |
"RILn" |
Recombinant inbred, n levels of selfing | As above, with phase-unknown heterozygotes coded
"X"
|
Missing scores are denoted "U" or "-" for
all population types.
mapDHf is an unconstructed doubled haploid marker set of
599 markers scored on 218 individuals, formatted for input to this
function.
testd <- mstmap(mapDHf, dist.fun = "kosambi", trace = FALSE, as.cross = TRUE)Number of linkage groups: 24
The size of the linkage groups are: 56 54 35 41 4 37 6 30 40 27 37 13 15 10 21 6 32 33 33 41 6 9 5 8
The number of bins in each linkage group: 55 53 34 41 3 36 6 29 40 27 36 13 14 9 21 5 32 33 32 41 5 8 4 7
nmar(testd) L1 L2 L3 L4 L5 L6 L7 L8 L9 L10 L11 L12 L13 L14 L15 L16 L17 L18 L19 L20
56 54 35 41 4 37 6 30 40 27 37 13 15 10 21 6 32 33 33 41
L21 L22 L23 L24
6 9 5 8
chrlen(testd) L1 L2 L3 L4 L5 L6 L7
142.806369 181.935011 97.376797 115.405242 21.660902 108.162200 13.256931
L8 L9 L10 L11 L12 L13 L14
133.885978 153.235513 98.705941 145.839837 60.441336 72.211612 81.224002
L15 L16 L17 L18 L19 L20 L21
98.211685 8.738474 109.472813 60.913640 134.491476 103.954898 18.019891
L22 L23 L24
7.801089 7.810474 19.196583 Setting as.cross = TRUE is recommended, since it returns
an R/qtl cross object of the appropriate class and thereby makes the
facilities of both packages available for subsequent work. The class
assigned depends on the population type.
pop.type |
Class assigned | Mechanism |
|---|---|---|
"BC" |
"bc" |
Direct |
"DH" |
"dh" |
Direct |
"ARIL" |
"riself" |
Direct |
"RILn" |
"bcsft" |
Via qtl::convert2bcsft() with F.gen = n,
BC.gen = 0
|
With as.cross = FALSE the map is returned instead as a
data frame carrying additional columns for the linkage group, marker
position and genetic distance.
Construction from a cross object
mstmap.cross()
accepts an unconstructed or constructed map held in an R/qtl cross
object, and is the more flexible of the two. The object must inherit one
of the classes "bc", "dh",
"riself" or "bcsft", a restriction that guards
against attempting construction for the more complex population types
R/qtl supports.
How these classes arise matters in practice.
read.cross() assigns the class "bc" to any
bi-parental population. Doubled haploid populations may be assigned
"dh" simply by changing the class; for the purpose of
construction the two are equivalent.
Non-advanced recombinant inbred populations require fully informative
markers, that is three distinct allele types, and
read.cross() will assign them the class "f2".
The level of selfing must then be encoded by conversion:
| Population | Conversion |
|---|---|
| Selfed times |
qtl::convert2bcsft(F.gen = n, BC.gen = 0), giving class
"bcsft"
|
| Genuine advanced RIL |
qtl::convert2riself(), giving class
"riself" and replacing any residual heterozygosity with
missing values |
The object is returned with the same class structure it was given, so that all functions of both packages remain applicable.
For both functions, the
p.valueargument governs the separation of markers into linkage groups and is strongly dependent on population size. Some experimentation is generally required. See Clustering markers into linkage groups for the relationship, which may be examined directly withpValue().
Modes of reconstruction
The constructed map mapDH illustrates the flexibility of
mstmap.cross(). Its 23 linkage groups are named, and the
markers within each are named according to their order.
nmar(mapDH) 1A 1B1 1B2 1D 2A 2B 2D1 2D2 3A 3B 3D 4A 4B 4D 5A 5B 5D 6A 6B 6D
41 5 33 10 40 35 8 13 37 30 6 30 32 6 54 56 6 27 41 15
7A 7B 7D
33 37 4
pull.map(mapDH)[[4]] 1D.m.1 1D.m.2 1D.m.3 1D.m.4 1D.m.5 1D.m.6 1D.m.7 1D.m.8
0.000000 2.285816 2.742698 2.742698 21.465574 25.652893 57.200980 58.104090
1D.m.9 1D.m.10
58.568087 81.061896
attr(,"class")
[1] "A"The four modes below are selected through bychr,
chr and anchor.
| Requirement | bychr |
chr |
Effect on linkage groups |
|---|---|---|---|
| Rebuild the entire map | FALSE |
unset | Re-clustered and renamed |
| Re-order within existing groups | TRUE |
unset | Retained, possibly split |
| Rebuild nominated groups only | FALSE |
set | Nominated groups re-clustered |
| Re-order nominated groups only | TRUE |
set | Nominated groups retained |
Complete reconstruction
Setting bychr = FALSE combines the marker data from all
linkage groups, re-clusters the markers and orders them within each
resulting group.
mapDHa <- 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
nmar(mapDHa) L.1 L.10 L.11 L.12 L.13 L.14 L.15 L.16 L.17 L.18 L.19 L.2 L.20 L.21 L.22 L.23
41 30 6 9 21 32 6 54 56 6 27 5 41 15 33 37
L.24 L.3 L.4 L.5 L.6 L.7 L.8 L.9
4 33 10 40 35 8 13 37
pull.map(mapDHa)[[4]] 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
attr(,"class")
[1] "A"The reconstructed map contains 24 linkage groups, the additional
group arising from a minor split in 4A. Because the map is built from
first principles the former linkage group names are discarded and a
standard "L." prefix applied. This example also shows that
MSTmap does not, by default, respect the marker order it was given.
Ordering within established groups
Where only the order within existing linkage groups is at issue, set
bychr = TRUE. Setting anchor = TRUE
additionally causes the inputted marker orders to be respected.
mapDHb <- mstmap(mapDH, bychr = TRUE, dist.fun = "kosambi", anchor = TRUE, 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
nmar(mapDHb) 1A 1B1 1B2 1D 2A 2B 2D1 2D2 3A 3B 3D 4A.1 4A.2 4B 4D 5A
41 5 33 10 40 35 8 13 37 30 6 9 21 32 6 54
5B 5D 6A 6B 6D 7A 7B 7D
56 6 27 41 15 33 37 4 The result is identical to mapDH except that 4A has been
split in two. As bychr = TRUE, the function recognises the
origin of the group and uses 4A as a prefix in naming the two new
groups.
Ordering without splitting
The split above arose solely from the default
p.value = 1e-06. Relaxing it keeps 4A intact.
mapDHc <- mstmap(mapDH, bychr = TRUE, dist.fun = "kosambi", anchor = TRUE,
trace = FALSE, p.value = 1e-04)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
nmar(mapDHc) 1A 1B1 1B2 1D 2A 2B 2D1 2D2 3A 3B 3D 4A 4B 4D 5A 5B 5D 6A 6B 6D
41 5 33 10 40 35 8 13 37 30 6 30 32 6 54 56 6 27 41 15
7A 7B 7D
33 37 4 The same result follows from p.value = 2, or any value
greater than unity, which instructs the algorithm not to split linkage
groups however weak the linkages within them.
Suppressing splitting entirely carries a cost. A linkage group containing sets of markers separated by a substantial distance, and therefore weakly linked, may suffer local orientation problems.
Reconstruction of nominated groups
Supplying chr together with bychr = FALSE
restricts complete reconstruction to the nominated linkage groups.
mapDHd <- mstmap(mapDH, chr = names(mapDH$geno)[1:3], bychr = FALSE,
dist.fun = "kosambi", trace = FALSE, p.value = 1e-04)Number of linkage groups: 3
The size of the linkage groups are: 41 5 33
The number of bins in each linkage group: 41 4 33
nmar(mapDHd) 1D 2A 2B 2D1 2D2 3A 3B 3D 4A 4B 4D 5A 5B 5D 6A 6B 6D 7A 7B 7D
10 40 35 8 13 37 30 6 30 32 6 54 56 6 27 41 15 33 37 4
L.1 L.2 L.3
41 5 33 Here too the original group names are discarded and new ones defined.
Setting bychr = TRUE instead orders markers within the
groups nominated by chr, and an appropriate
p.value will keep those groups unbroken.
Further reading
-
How the MSTmap algorithm works —
the basis of
objective.fun,p.value,mvest.bcanddetectBadData - Pulling and pushing markers — curating the marker set before construction
- Worked example I — construction applied to an unconstructed barley backcross
-
mstmap.cross(),mstmap.data.frame()— full argument documentation