getCnvp: getCnvp

In ICDS: Identification of Cancer Dysfunctional Subpathway with Omics Data

Description

'getCnvp' perform t-test on copy number variation data

Usage

getCnvp(
  exp_data,
  cnv_data,
  amp_gene,
  del_gene,
  p.adjust = TRUE,
  method = "fdr"
)

Arguments

exp_data	A data frame
cnv_data	Copy number variation data
amp_gene	A vector of strings, the IDs of amplified genes.
del_gene	A vector of strings, the IDs of deleted genes.
p.adjust	Logical,tell if returns corrected p-values
method	Correction method,which can be one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY",

Details

cnv_data is TCGA level4 data.if p.adjust=TRUE,return corrected p-values,if p.adjust=FALSE,return p-values

Value

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

Examples

exp_data<-GetExampleData("exp_data")
meth_data<-GetExampleData("meth_data")
cnv_data<-GetExampleData("cnv_data")
amp_gene<-GetExampleData("amp_gene")
del_gene<-GetExampleData(("del_gene"))
getCnvp(exp_data,cnv_data,amp_gene,del_gene,p.adjust=FALSE,method="fdr")

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