countGT: countGT

In ruqianl/comapr: Crossover analysis and genetic map construction

countGT

Description

count how many samples have genotypes calls across markers and count how many markers that each individual has called genotypes for. This function helps identify poor samples or poor markers for filtering. It can also generate plots that help identify outlier samples/markers

Usage

countGT(geno, plot = TRUE, interactive = FALSE)

Arguments

geno	the genotype data.frame of markers by samples from output of function correctGT
plot,	it determines whether a plot will be generated, defaults to TRUE
interactive,	it determines whether an interactive plot will be generated

Value

A list of two elements including n_markers and n_samples

Author(s)

Ruqian Lyu

Examples

data(snp_geno_gr)
genotype_counts <- countGT(GenomicRanges::mcols(snp_geno_gr))

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