dartR: gl.report.reproducibility – R documentation

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gl.report.reproducibility

Report summary of RepAvg (repeatability 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.reproducibility(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]

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.

Value

– Tabulation of repeatability against prospective Thresholds

Author(s)

Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

# SNP data
  out <- gl.report.reproducibility(testset.gl)
# Tag P/A data
  out <- gl.report.reproducibility(testset.gs)

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29