isSignificant: Finds Significant Regions

In MatthiasLienhard/qsea: IP-seq data analysis and vizualization

Finds Significant Regions

Description

This function looks for regions, where the test statistic is below the defined thresholds

Usage

isSignificant(glm, contrast = NULL, fdr_th = NULL, pval_th = NULL,
            absLogFC_th = NULL, direction = "both")

Arguments

glm	A qseaGLM object (mandatory)
contrast	name of contrast to be used
fdr_th	a threshold for the false discovery rate
pval_th	a p value threshold
absLogFC_th	the threshold for the absolute value of logFC
direction	direction of change: either "both", "loss", or "gain"

Details

If a threshold is NULL, it is ignored.

For the direction parameter, the following synonyms are valid:

"loss" == "less" == "hypo"

"gain" == "more" == "hyper"

Value

A vector with indices of significant windows, which can be passed to keep parameter of makeTable() function

Author(s)

Mathias Lienhard

See Also

makeTable

Examples

qs=getExampleQseaSet()
design=model.matrix(~group, getSampleTable(qs))
TvN_glm=fitNBglm(qs, design, norm_method="beta")
TvN_glm=addContrast(qs,TvN_glm, coef=2, name="TvN")
sig=isSignificant(TvN_glm, fdr_th=0.01)

MatthiasLienhard/qsea documentation built on March 22, 2023, 1:15 p.m.