Parameter initialization function
pp.init.RdParameter initialization function for pushCross and pullCross
Arguments
- seg.thresh
Numerical value between zero and one determining the p-value threshold for the test of marker segregation distortion.
- seg.ratio
A character string of the form "AA:BB" or "AA:AB:BB" describing the ratio of the alleles.
- miss.thresh
Numerical value between zero and one determining the proportion of missing values.
- max.rf
The maximum recombination fraction to consider when attempting to cluster pushed markers back into linkage groups.
- min.lod
The minimum LOD score to consider when attempting to cluster pushed markers back into linkage groups.
Details
This parameter initialization function is used by the function pullCross to
pull markers from a linkage map and pushCross to push markers
back into a linkage map. How the arguments seg.thresh,
seg.ratio and miss.thresh are used depends on which
function is called. See pushCross and pullCross for
more details.
References
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")
## pull markers from a linkage map with a segregation distortion
pars <- pp.init(seg.thresh = 0.05)
mapDH.s <- pullCross(mapDH, type = "seg.distortion", pars = pars)
mapDH.s$seg.distortion$table
#> mark chr pos neglog10P missing AA AB
#> 1 1A.m.26 1A 68.4700927 1.375015 0.000000000 0.5688073 0.4311927
#> 2 1A.m.27 1A 70.3026255 1.375015 0.000000000 0.5688073 0.4311927
#> 3 1A.m.29 1A 73.9768038 1.671789 0.000000000 0.5779817 0.4220183
#> 4 1A.m.30 1A 75.8125081 1.375015 0.000000000 0.5688073 0.4311927
#> 5 1A.m.32 1A 76.4333654 1.519835 0.000000000 0.5733945 0.4266055
#> 6 1A.m.33 1A 76.8921092 1.671789 0.000000000 0.5779817 0.4220183
#> 7 1A.m.34 1A 77.3500443 1.830929 0.000000000 0.5825688 0.4174312
#> 8 1A.m.35 1A 85.1907512 1.375015 0.000000000 0.5688073 0.4311927
#> 9 1A.m.36 1A 89.7685841 1.375015 0.000000000 0.5688073 0.4311927
#> 10 1A.m.37 1A 91.1441558 1.830929 0.000000000 0.5825688 0.4174312
#> 11 1A.m.38 1A 98.0699737 1.671789 0.000000000 0.5779817 0.4220183
#> 12 1A.m.39 1A 100.3648637 1.519835 0.000000000 0.5733945 0.4266055
#> 13 1A.m.40 1A 100.8234047 1.671789 0.000000000 0.5779817 0.4220183
#> 14 1A.m.41 1A 101.2722224 1.519835 0.000000000 0.5733945 0.4266055
#> 15 2A.m.1 2A 0.0000000 1.375015 0.000000000 0.5688073 0.4311927
#> 16 2A.m.9 2A 51.3456384 1.671789 0.000000000 0.5779817 0.4220183
#> 17 2A.m.29 2A 104.8080733 1.338322 0.032110092 0.5687204 0.4312796
#> 18 2D2.m.1 2D2 0.0000000 1.519835 0.000000000 0.5733945 0.4266055
#> 19 2D2.m.2 2D2 0.4488151 1.375015 0.000000000 0.5688073 0.4311927
#> 20 2D2.m.3 2D2 0.9317667 1.600692 0.004587156 0.5760369 0.4239631
#> 21 3A.m.16 3A 64.3531474 1.375015 0.000000000 0.5688073 0.4311927
#> 22 3A.m.17 3A 64.8121744 1.451708 0.004587156 0.5714286 0.4285714
#> 23 3A.m.19 3A 79.4373752 1.375015 0.000000000 0.5688073 0.4311927
#> 24 3B.m.15 3B 64.1925357 1.997307 0.000000000 0.5871560 0.4128440
#> 25 3B.m.16 3B 64.6508816 2.170970 0.000000000 0.5917431 0.4082569
#> 26 3B.m.17 3B 65.1096201 1.872327 0.027522936 0.5849057 0.4150943
#> 27 3B.m.18 3B 65.1096202 1.997307 0.000000000 0.5871560 0.4128440
#> 28 3B.m.19 3B 65.5683123 1.830929 0.000000000 0.5825688 0.4174312
#> 29 3B.m.20 3B 66.4854592 1.830929 0.000000000 0.5825688 0.4174312
#> 30 3B.m.23 3B 79.3776517 1.600692 0.004587156 0.5760369 0.4239631
#> 31 4B.m.1 4B 0.0000000 1.600692 0.004587156 0.5760369 0.4239631
#> 32 4B.m.2 4B 17.7567993 1.519835 0.000000000 0.5733945 0.4266055
#> 33 4B.m.5 4B 28.3629008 1.671789 0.000000000 0.5779817 0.4220183
#> 34 4B.m.6 4B 31.1069464 1.375015 0.000000000 0.5688073 0.4311927
#> 35 5B.m.31 5B 104.6713214 1.375015 0.000000000 0.5688073 0.4311927
#> 36 5B.m.32 5B 105.5889034 1.375015 0.000000000 0.5688073 0.4311927
#> 37 5B.m.33 5B 106.0475396 1.519835 0.000000000 0.5733945 0.4266055
#> 38 5B.m.35 5B 107.4238503 1.375015 0.000000000 0.5688073 0.4311927
#> 39 6D.m.12 6D 60.6944586 1.756872 0.004587156 0.4193548 0.5806452
#> 40 7B.m.6 7B 23.0304066 1.769873 0.013761468 0.4186047 0.5813953
#> 41 7B.m.7 7B 23.2002891 1.309862 0.004587156 0.4331797 0.5668203