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 1.4.0 Index]