netgwas (version 1.14.3)

cal.pos: Estimate genetic map distances

Description

Calculation of genetic map distances for an estimated markers order from either net.map or buildMap functions. This function is only for diploid populations. We note that the output of net.map and buildMap functions include estimated linkage groups and estimated markers order within each linkage group.

Usage

cal.pos (netgwasmap, pop.type= NULL , map.func = "haldane", chr )

Value

The netgwas constructed linkage map is returned as a R/qtl cross object. The object is a list with usual components "pheno" and "geno".

geno

The "geno" element contains data and map for separated linkage groups which have been constructed using net.map function.

pheno

Character string containing the genotype names.

Arguments

netgwasmap

A netgwasmap object. The output of netmap or buildMap functions.

pop.type

Character string specifying the population type of the genotype data. Accepted values are "DH" (doubled haploid), "BC" (backcross), "RILn" (non-advanced RIL population with n generations of selfing) and "ARIL" (advanced RIL) (see Details).

map.func

Character string defining the distance function used for calculation of genetic distances. Options are "kosambi", "haldane", and "morgan". Default is "haldane".

chr

A character string of linkage group names that require calculating of their genetic map distances.

Author

Pariya Behrouzi
Maintainer: Pariya Behrouzi

Details

In qtl package, the genotype data for a backcross is coded as NA = missing, 1 = AA, 2 = AB. For an F2 intercross, the coding is NA = missing, 1 = AA, 2 = AB, 3 = BB, 4 = not BB (i.e. AA or AB), 5 = not AA (i.e. AB or BB).

If pop.typ = "RILn" the number of generations of selfing is limited to 20 to ensure sensible input. The constructed object is returned as a R/qtl cross object with the appropriate class structure. For "RILn" populations the constructed object is given the class "bcsft" by using the qtl package conversion function convert2bcsft with arguments F.gen = n and BC.gen = 0. For "ARIL" populations the constructed object is given the class "riself".

This function uses the Viterbi algorithm implemented in argmax.geno of the qtl package to estimate genetic distances. Initial conservative estimates of the map distances are calculated from inverting recombination fractions outputted from est.rf. These are then passed to argmax.geno and imputation of missing allele scores is performed along with re-estimation of map distances. This is an adapted version of quickEst function from ASMap package.

Examples

if (FALSE) {
sim <- simRIL(d=25, n=200, g=5, cM=100, selfing= 2)
 # to use the same genotyping coding as qtl package (See details)
sim$data <- (sim$data) + 1 

 #Estimate linkage groups and order markers within each LG
out <- netmap(sim$data, cross = "inbred")
map <- out$map; map

plot(out)

 #Calculate map positions and convert the map to cross object from qtl package
pos.map <- cal.pos(netgwasmap = out, pop.type= "RIL2", map.func = "haldane" )
plotMap(pos.map)
}