filterSegreg | R Documentation |
Filter genotypes based on the chi2 statistic to test for segregation distortion.
filterSegreg(
x,
thresh.pval = 0.05,
return.counts = FALSE,
is.F2 = FALSE,
nb.cores = 1,
verbose = 1
)
x |
data.frame similar to the output from |
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 |
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) |
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
)
Timothee Flutre
genoClasses2JoinMap
, updateJoinMap
, plotHistPval
, qqplotPval
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