readSegment: readSegment

In Niinleslie/MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Description

readSegment

Usage

readSegment(
  segFile,
  gisticAmpGenesFile = NULL,
  gisticDelGenesFile = NULL,
  gisticAllLesionsFile = NULL,
  gistic.qval = 0.25,
  min.seg.size = 500,
  txdb = NULL,
  min.overlap.len = 50,
  verbose = TRUE,
  ...
)

Arguments

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 cna2gene.

Value

a list of segmentation data frame

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)

Niinleslie/MesKit documentation built on Jan. 29, 2022, 10:24 a.m.