readGistic: Read and summarize gistic output.

In maftools: Summarize, Analyze and Visualize MAF Files

Description

A little function to summarize gistic output files. Summarized output is returned as a list of tables.

Usage

readGistic(
  gisticAllLesionsFile = NULL,
  gisticAmpGenesFile = NULL,
  gisticDelGenesFile = NULL,
  gisticScoresFile = NULL,
  cnLevel = "all",
  isTCGA = FALSE,
  verbose = TRUE
)

Arguments

gisticAllLesionsFile	All Lesions file generated by gistic. e.g; all_lesions.conf_XX.txt, where XX is the confidence level. Required. Default NULL.
gisticAmpGenesFile	Amplification Genes file generated by gistic. e.g; amp_genes.conf_XX.txt, where XX is the confidence level. Default NULL.
gisticDelGenesFile	Deletion Genes file generated by gistic. e.g; del_genes.conf_XX.txt, where XX is the confidence level. Default NULL.
gisticScoresFile	scores.gistic file generated by gistic.
cnLevel	level of CN changes to use. Can be 'all', 'deep' or 'shallow'. Default uses all i.e, genes with both 'shallow' or 'deep' CN changes
isTCGA	Is the data from TCGA. Default FALSE.
verbose	Default TRUE

Details

Requires output files generated from GISTIC. Gistic documentation can be found here ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTICDocumentation_standalone.htm

Value

A list of summarized data.

Examples

all.lesions <- system.file("extdata", "all_lesions.conf_99.txt", package = "maftools")
amp.genes <- system.file("extdata", "amp_genes.conf_99.txt", package = "maftools")
del.genes <- system.file("extdata", "del_genes.conf_99.txt", package = "maftools")
scores.gistic <- system.file("extdata", "scores.gistic", package = "maftools")
laml.gistic = readGistic(gisticAllLesionsFile = all.lesions, gisticAmpGenesFile = amp.genes, gisticDelGenesFile = del.genes, gisticScoresFile = scores.gistic, isTCGA = TRUE)

Example output

-Processing Gistic files..
--Processing amp_genes.conf_99.txt
--Processing del_genes.conf_99.txt
--Processing scores.gistic
--Summarizing by samples

maftools documentation built on Feb. 6, 2021, 2 a.m.