readGistic {maftools} | R Documentation

## Read and summarize gistic output.

### 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)

[Package maftools version 2.10.05 Index]