cna2gene: cna2gene

In MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Description

cna2gene

Usage

cna2gene(seg, txdb, min.overlap.len = 50, geneList = NULL)

Arguments

seg	seg object generated by readSegment function.
txdb	A TxDb object. i.e., TxDb.Hsapiens.UCSC.hg19.knownGene. Default NULL.
min.overlap.len	The minimum insertion size of segment and gene. Default 50.
geneList	The list of genes used to limit the annotation.Default NULL.

Value

seg object

Examples

segFile <- system.file("extdata", "CRC_HZ.seg.txt", package = "MesKit")
gisticAmpGenesFile <- system.file("extdata", "COREAD_amp_genes.conf_99.txt", package = "MesKit")
gisticDelGenesFile <- system.file("extdata", "COREAD_del_genes.conf_99.txt", package = "MesKit")
gisticAllLesionsFile <- system.file("extdata", "COREAD_all_lesions.conf_99.txt", package = "MesKit")
seg <- readSegment(segFile = segFile,
                   gisticAmpGenesFile = gisticAmpGenesFile,
                    gisticDelGenesFile = gisticDelGenesFile, 
                   gisticAllLesionsFile = gisticAllLesionsFile)
                   
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
cna2gene(seg, txdb = TxDb.Hsapiens.UCSC.hg19.knownGene)

MesKit documentation built on March 28, 2021, 6 p.m.