getMethp: getMethp

In ICDS: Identification of Cancer Dysfunctional Subpathway with Omics Data

getMethp

Description

'getMethp' perform t-test on Methylation profile data

Usage

getMethp(meth_data, label, p.adjust = TRUE, method = "fdr")

Arguments

meth_data	A data frame, the Methylation profile to calculate p-value for each gene, the rownames should be the symbol of genes.
label	label A vector of 0/1s, indicating the class of samples in the Methylation 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 Methylation 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 Methylation profile should be gene symbols and the column of the Methylation 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("meth_data")
label<-GetExampleData("label2")
getMethp(profile,label,p.adjust=FALSE)

ICDS documentation built on Sept. 11, 2024, 6:32 p.m.