getExpp: getExpp

In ICDS: Identification of Cancer Dysfunctional Subpathway with Omics Data

Description

'getExpp' perform t-test on Expression profile data

Usage

getExpp(exp_data, label, p.adjust = TRUE, method = "fdr")

Arguments

exp_data	A data frame, the expression profile to calculate p-value for each gene, the rownames should be the symbol of genes.
label	A vector of 0/1s, indicating the class of samples in the expression profile, 0 represents case, 1 represents control.
p.adjust	Logical,tell if returns corrected p-values
method	Correction method,which can be one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY",

Details

For a given expression profile of two conditions, ICDS package provide t-test method to calculate p-values or corrected p-values(if p.adjust=TRUE,return corrected p-values,if p.adjust=FALSE,return p-values.) for each genes. The row of the expression profile should be gene symbols and the column of the expression profile should be names of samples. Samples should be under two conditions and the label should be given as 0 and 1.

Value

A numeric vector of p-values or corrected p-values

Examples

profile<-GetExampleData("exp_data")
label<-GetExampleData("label1")
getExpp(profile,label,p.adjust=FALSE)

ICDS documentation built on July 15, 2021, 5:06 p.m.