calc_errorlod {qtl2} | R Documentation |
Calculate genotyping error LOD scores
Description
Use the genotype probabilities calculated with
calc_genoprob()
to calculate genotyping error LOD
scores, to help identify potential genotyping errors (and problem
markers and/or individuals).
Usage
calc_errorlod(cross, probs, quiet = TRUE, cores = 1)
Arguments
cross |
Object of class |
probs |
Genotype probabilities as calculated from |
quiet |
If |
cores |
Number of CPU cores to use, for parallel calculations.
(If |
Details
Let O_k
denote the observed marker genotype at position
k
, and g_k
denote the corresponding true underlying
genotype.
Following Lincoln and Lander (1992), we calculate
LOD = log_{10} [ Pr(O_k | g_k = O_k) / Pr(O_k | g_k \ne O_K) ]
Value
A list of matrices of genotyping error LOD scores. Each matrix corresponds to a chromosome and is arranged as individuals x markers.
References
Lincoln SE, Lander ES (1992) Systematic detection of errors in genetic linkage data. Genomics 14:604–610.
See Also
Examples
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
probs <- calc_genoprob(iron, error_prob=0.002, map_function="c-f")
errorlod <- calc_errorlod(iron, probs)
# combine into one matrix
errorlod <- do.call("cbind", errorlod)