dartR (version 1.9.9.1)

gl.report.RepAvg: Report summary of RepAvg averaged over both alleles for each locus or reproducibility (repeatability of the scores for fragment presence/absence).

Description

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

Usage

gl.report.RepAvg(x, boxplot = "adjusted", range = 1.5, verbose = NULL)

Arguments

x

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

boxplot

-- if 'standard', plots a standard box and whisker plot; if 'adjusted', plots a boxplot adjusted for skewed distributions [default 'adjusted']

range

-- specifies the range for delimiting outliers [default = 1.5 interquartile ranges]

verbose

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

Value

-- Tabulation of repeatability against prospective Thresholds

Details

In the case of fragment presence/absence data (SilicoDArT), repeatability is the percentage of scores that are repeated in the technical replicate dataset.

A histogram and whisker plot are produced to aid in selecting a threshold.

Examples

# NOT RUN {
# SNP data
  out <- gl.report.reproducibility(testset.gl)
# Tag P/A data
  out <- gl.report.reproducibility(testset.gs)
# }