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

In GeoTcgaData: Processing various types of data on GEO and TCGA

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

## Not run: 
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)

## End(Not run)

GeoTcgaData documentation built on Sept. 23, 2022, 9:05 a.m.