diff_SNP_tcga: Do difference analysis of SNP data downloaded from...

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

Do difference analysis of SNP data downloaded from TCGAbiolinks

Description

Do difference analysis of SNP data downloaded from TCGAbiolinks

Usage

diff_SNP_tcga(snpData, sampleType)

Arguments

snpData	data.frame of SNP data downloaded from TCGAbiolinks
sampleType	vector of sample group

Examples

## Not run: 
library(TCGAbiolinks)
query <- GDCquery(
    project = "TCGA-CHOL", 
    data.category = "Simple Nucleotide Variation", 
    access = "open", 
    legacy = FALSE, 
    data.type = "Masked Somatic Mutation", 
    workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking"
)
GDCdownload(query)
data_snp <- GDCprepare(query)
samples <- unique(data_snp$Tumor_Sample_Barcode)
sampleType <- sample(c("A","B"), length(samples), replace = TRUE)
names(sampleType) <- samples
pvalue <- diff_SNP_tcga(snpData = data_snp, sampleType = sampleType)

## End(Not run)

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