compFscore: F score computation

In guigolab/sQTLseekeR2: R package for splicing QTL mapping

Description

Compute the F score, max diff ratio difference and transcripts that change the most. Additionally, it can compute a P-value to assess the significance of the F score.

Usage

compFscore(geno.df, tre.mt, svQTL = FALSE, asympt = TRUE, res = FALSE)

Arguments

geno.df	a data.frame of one row with the genotype information for each sample.
tre.mt	a matrix with the transcript relative expression (samples x transcripts).
svQTL	should svQTL test be performed in addition to sQTL. Default is FALSE.
asympt	should significance for the F score (sQTL test) be computed using the davies method in the CompQuadForm package. Default is TRUE.
res	is tre.mt the residual of the regression of additional covariates. Default is FALSE

Value

A data.frame with columns:

F	the F score.
nb.groups	the number of genotype groups.
md	the maximum difference in splicing ratios between genotype groups.
tr.first, tr.second	the two transcripts that change the most.
info	comma separated list with the number of individuals per genotype group: -1,0,1,2.
pv	if asympt is TRUE a P-value for the F score is computed.

Author(s)

Diego Garrido-Martín, Jean Monlong

guigolab/sQTLseekeR2 documentation built on Nov. 20, 2021, 3:21 a.m.