find.de.genes: Find differentially expressed genes

In emreg00/pepper: PErsonalized Perturbation ProfilER

Description

Find differentially expressed genes

Usage

find.de.genes(expr, sample.mapping, states, method = "limma",
  out.file = NULL, state.background = NULL, adjust.method = "BH",
  cutoff = 0.05, functional.enrichment = NULL)

Arguments

expr	expression matrix.
sample.mapping	Sample - condition mapping.
states	Conditions to be considered as case.
method	Differential expression analysis method: limma (Default) | sam | welch.
out.file	File to write output. If NULL (default) not used.
state.background	Condition to be considered as control.
adjust.method	Multiple hypothesis testing correction method. Defaults to BH.
cutoff	Adjust p-value cutoff. Defaults to 0.05
functional.enrichment	GO or KEGG based functional enrichment analysis

Value

data frame with results

Examples

gds.data = fetch.expression.data("GDS4966", do.log2=F, probe.conversion="Gene ID")
expr = gds.data$expr
sample.mapping = gds.data$sample.mapping
sample.mapping = convert.sample.mapping.to.case.control(sample.mapping,
 		    states.control = c("healthy donor"), 
		    states.case = c("tuberculosis", "latent tuberculosis infection"))
d = find.de.genes(expr, sample.mapping, c("case", "control"), method="limma")

emreg00/pepper documentation built on May 16, 2019, 5:10 a.m.