getDistortedMarkers: getDistortedMarkers

In ruqianl/comapr: Crossover analysis and genetic map construction

getDistortedMarkers

Description

Marker segregation distortion detection using chisq-test

Usage

getDistortedMarkers(geno, p = c(0.5, 0.5), adj.method = "BH")

Arguments

geno	the genotype data.frame of markers by samples from output of function correctGT
p	the expected geneotype ratio in a numeric vector, defaults to c(0.5,0.5)
adj.method	Methods to adjust for multiple comparisons, defaults to "BH"

Details

We expect the genotypes to appear with the frequencies of 1:1 homo_alt:hets. We usechisq.test for finding markers that have genotypes among samples that are significantly different from the 1:1 ratio and report them

Value

data.frame with each row representing one SNP marker and columns containing the chisq.test results

Author(s)

Ruqian Lyu

Examples

data(parents_geno)
data(snp_geno_gr)
corrected_geno <- correctGT(gt_matrix = GenomicRanges::mcols(snp_geno_gr),
ref = parents_geno$ref,alt = parents_geno$alt,fail = "Fail",
wrong_label = "Homo_ref")
GenomicRanges::mcols(snp_geno_gr) <- corrected_geno
corrected_geno <- filterGT(snp_geno_gr, min_markers = 30,min_samples = 2)
pvalues <- getDistortedMarkers(GenomicRanges::mcols(corrected_geno))

ruqianl/comapr documentation built on Oct. 27, 2023, 5:12 a.m.