compPvalue: P-values computation.

In dgarrimar/sQTLseekeR2: R package for splicing QTL mapping

Description

Compute P-values from F scores using the methods available in the vegan package. Method adonis is used for sQTL testing and method betadisper for svQTLs.

Usage

compPvalue(
  res.df,
  tre.mt,
  min.nb.ext.scores = 1000,
  nb.perm.max = 1e+06,
  svQTL = FALSE
)

Arguments

res.df	a data.frame with the F scores and number of groups.
tre.mt	a matrix with the transcript relative expression (samples x transcripts).
min.nb.ext.scores	the minimum number of permuted scores higher than 'F.lead' to allow the computation to stop. Default is 1000.
nb.perm.max	the maximum number of permutations. Default is 1e6.
svQTL	should svQTL test be performed instead of sQTL. Default is FALSE.

Value

An updated data.frame res.df with new columns 'pv' and 'nb.perms'.

Author(s)

Diego Garrido-Martín, Jean Monlong

dgarrimar/sQTLseekeR2 documentation built on Nov. 22, 2021, 3:23 a.m.