GeoTcgaData (version 1.1.1.992)

diff_CNV: Do difference analysis of gene level copy number variation data

Description

Do difference analysis of gene level copy number variation data

Usage

diff_CNV(cnvData, sampleGroup, ...)

Arguments

cnvData

data.frame of CNV data

sampleGroup

vector of sample group

...

parameters for fisher.test

Examples

if (FALSE) {
library(TCGAbiolinks)
query <- GDCquery(project = "TCGA-LGG",
                  data.category = "Copy Number Variation",
                  data.type = "Gene Level Copy Number Scores")

GDCdownload(query, method = "api", files.per.chunk = 5, directory = Your_Path)
data <- GDCprepare(query = query, 
                   save = TRUE, 
                   directory =  "Your_Path") 

class(data) <- "data.frame"
cnvData <- data[, -c(1,2,3)]
rownames(cnvData) <- data[, 1]
sampleGroup  = sample(c("A","B"), ncol(cnvData), replace = TRUE)
diffCnv <- diff_CNV(cnvData, sampleGroup)
}