filterSegreg: Filter for segregation

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Filter for segregation

Description

Filter genotypes based on the chi2 statistic to test for segregation distortion.

Usage

filterSegreg(
  x,
  thresh.pval = 0.05,
  return.counts = FALSE,
  is.F2 = FALSE,
  nb.cores = 1,
  verbose = 1
)

Arguments

x	data.frame similar to the output from genoClasses2JoinMap, with locus in rows and where the first columns corresponding to parents are discarded, i.e. the first column should be named "seg" and the following should correspond to offsprings
thresh.pval	significance threshold at which to control the FWER (Bonferroni-adjusted p values) and the FDR (Benjamini-Hochberg-adjusted p values); the number of non-rejected null hypotheses will be shown only if verbose is non-zero
return.counts	if TRUE, counts used to calculate the chi2 statistic are returned
is.F2	if TRUE, it is assumed that the two outbred parents were crossed once to make a F1 which was then autofecundated multiple times to make the offsprings; note that the SNP genotypes of the F1 should not be given (and they are often unavailable)
nb.cores	the number of cores to use, i.e. at most how many child processes will be run simultaneously (not on Windows)
verbose	verbosity level (0/1)

Value

data.frame with one row per locus and several columns (chi2, p value, Bonferroni-adjusted p value, Benjamini-Hochberg-adjusted p value), as well as counts (if return.counts=TRUE)

Author(s)

Timothee Flutre

See Also

genoClasses2JoinMap, updateJoinMap, plotHistPval, qqplotPval

timflutre/rutilstimflutre documentation built on Aug. 18, 2024, 7:43 p.m.