readGistic: Read and summarize gistic output.

Description Usage Arguments Details Value Examples

View source: R/readGistic.R

Description

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

Usage

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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

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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.