tmodLimmaDecideTests: Up- and down-regulated genes in modules based on limma object

In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Up- and down-regulated genes in modules based on limma object

Description

For each module in mset and for each coefficient in f$coefficients, this function calculates the numbers of significantly up- and down-regulated genes.

Usage

tmodLimmaDecideTests(
  f,
  genes,
  lfc.thr = 0.5,
  pval.thr = 0.05,
  filter.unknown = FALSE,
  adjust.method = "BH",
  mset = "all"
)

Arguments

f	result of linear model fit produced by limma functions lmFit and eBayes
genes	Either the name of the column in f$genes which contains the gene symbols corresponding to the gene set collection used, or a character vector with gene symbols
lfc.thr	log fold change threshold
pval.thr	p-value threshold
filter.unknown	If TRUE, modules with no annotation will be omitted
adjust.method	method used to adjust the p-values for multiple testing. See p.adjust(). Default:BH.
mset	Which module set to use (see tmodUtest for details)

Details

For an f object returned by eBayes(), tmodLimmaDecideTests considers every coefficient in this model (every column of f$coefficients). For each such coefficient, tmodLimmaDecideTests calculates, for each module, the number of genes which are up- or down-regulated.

In short, tmodLimmaDecideTests is the equivalent of tmodDecideTests, but for limma objects returned by eBayes().

Value

A list with as many elements as there were coefficients in f. Each element of the list is a data frame with the columns "Down", "Zero" and "Up" giving the number of the down-, not- and up-regulated genes respectively. Rows of the data frame correspond to module IDs. The object can directly be used in tmodPanelPlot as the pie parameter.

See Also

tmodDecideTests, tmodLimmaTest, tmodPanelPlot

Examples

## Not run: 
data(Egambia)
design <- cbind(Intercept=rep(1, 30), TB=rep(c(0,1), each= 15))
if(require(limma)) {
  fit <- eBayes( lmFit(Egambia[,-c(1:3)], design))
  ret <- tmodLimmaTest(fit, Egambia$GENE_SYMBOL)
  pie <- tmodLimmaDecideTests(fit, Egambia$GENE_SYMBOL)
  tmodPanelPlot(ret, pie=pie)
}

## End(Not run)

tmod documentation built on March 31, 2023, 9 p.m.