detect.err {netgwas}

Identiying likely genotyping error

Description

Calculates a LOD score for each genotype, measuring the evidence for genotyping errors. This uses calc.errorlod function from R/qtl package.

Usage

detect.err(netgwas.map,  err.prob= 0.01, cutoff= 4, 
          pop.type= NULL, map.func= "haldane")

Arguments

netgwas.map

An object of class netgwasmap object (The output of netmap or netmap functions).

err.prob

Assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype).

cutoff

Only those genotypes with error LOD scores above this cutoff will be listed.

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".

Value

A data.frame with 4 columns, whose rows correspond to the genotypes that are possibly in error. The four columns give the chromosome number, individual number, marker name, and error LOD score.

Examples

## Not run: 
sim <- simRIL(d=25, n=200, g=5, cM=100, selfing= 2)
 # to use the same genotyping coding as R/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)

# A list of genotyoing error
detect.err(out, pop.type = "RIL2")

## End(Not run)