filt_snps: Filter SNPs

Description Usage Arguments Value Examples

View source: R/filter.R

Description

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

Usage

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filt_snps(dat, filt)

## S3 method for class 'raw_data'
filt_snps(dat, filt)

## S3 method for class 'norm_data'
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

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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))])
}

grafab/gsrc documentation built on May 14, 2017, 3 p.m.