diff_SNP_tcga | R Documentation |
Do difference analysis of SNP data downloaded from TCGAbiolinks
diff_SNP_tcga(snpData, sampleType)
snpData |
data.frame of SNP data downloaded from TCGAbiolinks |
sampleType |
vector of sample group |
## 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)
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