readSegment {MesKit} | R Documentation |
readSegment
readSegment( segFile, gisticAmpGenesFile = NULL, gisticDelGenesFile = NULL, gisticAllLesionsFile = NULL, gistic.qval = 0.25, min.seg.size = 500, txdb = NULL, min.overlap.len = 50, verbose = TRUE, ... )
segFile |
The segment file. |
gisticAmpGenesFile |
Amplification Genes file generated by GISTIC. Default NULL. |
gisticDelGenesFile |
Deletion Genes file generated by GISTIC. Default NULL. |
gisticAllLesionsFile |
Information of all lesions generated by GISTIC. Default NULL. |
gistic.qval |
The threshold of gistic Q value. Default 0.25. |
min.seg.size |
The smallest size of segments. Default 500. |
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. |
verbose |
Whether to display details in the console. Default TRUE. |
... |
... Other options passed to |
a list of segmentation data frame
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)