is_hom: Who are the homozygous/heterozygous samples?

In maialab/daeqtlr: DAEQTL Mapping

Who are the homozygous/heterozygous samples?

Description

This function determines who are the homozygous or heterozygous samples given a data table of zygosity levels and a SNP of interest. Samples whose zygosity level is NA will be returned as FALSE.

Usage

is_hom(zygosity, snp, na_as_false = TRUE)

is_het(zygosity, snp, na_as_false = TRUE)

Arguments

zygosity	A data frame of zygosity levels: "hom" for homozygous or "het" for heterozygous. Each row is for a locus. The locus identity is indicated in the first column and named snp. Remaining columns are samples.
snp	String with SNP identifier.
na_as_false	Whether to return FALSE when the zygosity level is NA.

Value

A logical vector.

Examples

# Let us start by reading in an example data set with zygosity levels
zygosity <- read_snp_zygosity(file = daeqtlr_example("zygosity.csv"))

# Checking out SNP rsX005
zygosity['rsX005']
is_hom(zygosity, 'rsX005')
is_het(zygosity, 'rsX005')

# Translate the logical vector to sample names
# Note that first column is excluded because it is the SNP identifier col
# Homozygous samples
(homs <- colnames(zygosity)[-1][is_hom(zygosity, 'rsX005')])

# Heterozygous samples
(hets <- colnames(zygosity)[-1][is_het(zygosity, 'rsX005')])

# Some samples are neither homozygous nor heterozygous because of NAs
# Note the `- 1` because the first column of `zygosity` is the SNP identifier.
(ncol(zygosity) - 1) - length(c(homs, hets))

# The samples whose zygosity is NA are:
setdiff(colnames(zygosity)[-1], c(homs, hets))

maialab/daeqtlr documentation built on May 18, 2022, 6:53 a.m.