cna2gene: cna2gene

Description Usage Arguments Value Examples

View source: R/cna2gene.R

Description

cna2gene

Usage

1
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

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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.