cna2gene {MesKit}R Documentation

cna2gene

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)

[Package MesKit version 1.0.1 Index]