cna2gene {MesKit} | R Documentation |
cna2gene
cna2gene(seg, txdb, min.overlap.len = 50, geneList = NULL)
seg |
seg object generated by |
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. |
seg object
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)