gsrc (version 1.1)

filt_snps: Filter SNPs

Description

Some SNPs do not work as well as others and might be filtered out.

Usage

filt_snps(dat, filt)
"filt_snps"(dat, filt)
"filt_snps"(dat, filt)

Arguments

dat

Matrix with raw data or list with intensity, theta, position and chromosome objects.

filt

Character or numberic vector with SNP names or rownumbers to filter out.

Value

Filtered matrix.

Examples

if(require(brassicaData)){
data("raw_napus", package = "brassicaData", envir = environment())

dat <- intens_theta(raw_napus)
dat <- remove_suffix(dat, "_Grn")
dat <- geno_baf_rratio(dat, delthresh = 11)
dat <- filt_snps(dat, dat$snps[is.na(rowMeans(dat$baf, na.rm = TRUE))])
}