dartR (version 1.0.5)

gl.filter.repavg: Filter loci in a genlight {adegenet} object based on average reproducibility of alleles at a locus

Description

SNP datasets generated by DArT have in index, RepAvg, generated by reproducing the data independently for 30% of loci. RepAvg is the proportion of alleles that give a reproducible result, averaged over both alleles for each locus.

Usage

gl.filter.repavg(x, t = 1, v = 2)

Arguments

x

-- name of the genlight object containing the SNP data [required]

t

-- threshold value below which loci will be removed [default 0.95]

v

-- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2]

Value

Returns a genlight object retaining loci with a RepAvg greater than the specified threshold deleted.

Examples

# NOT RUN {
gl.report.repavg(testset.gl)
result <- gl.filter.repavg(testset.gl, t=0.95, v=3)
# }