map_cnv: This function maps cnv data to genes.

In oncoPredict: Drug Response Modeling and Biomarker Discovery

This function maps cnv data to genes.

Description

This function maps cnv data to genes.

Usage

map_cnv(Cnvs, folder = FALSE)

Arguments

Cnvs	The cnv data. A table with the following colnames: Sample (named using the TCGA patient barcode), Chromosome, Start, End, Num_Probes, and Segment_Mean.
folder	If TRUE, write a map.RData file containing the mapped CNV matrix and tumor sample indices. The default is FALSE.

Value

A list containing theCnvQuantVecList_mat (rows are genes, columns are samples) and tumorSamps (primary tumor/01A sample column indices).

Examples

if (requireNamespace("org.Hs.eg.db", quietly=TRUE) &&
    requireNamespace("TxDb.Hsapiens.UCSC.hg19.knownGene", quietly=TRUE)) {
  cnvData <- data.frame(Sample="TCGA-01-0001-01A-01D-0000-01",
                        Chromosome=7,
                        Start=55000000,
                        End=55200000,
                        Num_Probes=10,
                        Segment_Mean=1.5)
  mapped <- map_cnv(cnvData)
  names(mapped)
}

oncoPredict documentation built on June 29, 2026, 5:07 p.m.