isSignificant: Finds Significant Regions

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/qsea.makeTable.R

Description

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

Usage

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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

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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)

qsea documentation built on Nov. 8, 2020, 8:28 p.m.