filt_snps: Filter SNPs
In grafab/gsrc: Genome Structure Rearrangement Calling in Genomes with High Synteny

Description Usage Arguments Value Examples

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

filt_snps(dat, filt)

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

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

`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.

Filtered matrix.

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))])
}