Description Usage Arguments Details Value References See Also Examples
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).
1 | calc_errorlod(cross, probs, quiet = TRUE, cores = 1)
|
cross |
Object of class |
probs |
Genotype probabilities as calculated from |
quiet |
If |
cores |
Number of CPU cores to use, for parallel calculations.
(If |
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 = log10[ Pr(O[k] | g[k] = O[k]) / Pr(O[k] | g[k] != O[k]) ]
A list of matrices of genotyping error LOD scores. Each matrix corresponds to a chromosome and is arranged as individuals x markers.
Lincoln SE, Lander ES (1992) Systematic detection of errors in genetic linkage data. Genomics 14:604–610.
1 2 3 4 5 6 | iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2geno"))
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)
|
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