import.GISTIC {TRONCO} | R Documentation

## import.GISTIC

### Description

Transform GISTIC scores for CNAs in a TRONCO compliant object. Input can be either a matrix, with columns for each altered gene and rows for each sample; in this case colnames/rownames mut be provided. If input is a character an attempt to load a table from file is performed. In this case the input table format should be constitent with TCGA data for focal CNA; there should hence be: one column for each sample, one row for each gene, a column Hugo_Symbol with every gene name and a column Entrez_Gene_Id with every gene\'s Entrez ID. A valid GISTIC score should be any value of: "Homozygous Loss" (-2), "Heterozygous Loss" (-1), "Low-level Gain" (+1), "High-level Gain" (+2). For details and examples regarding the loading functions provided by the package we refer to the Vignette Section 3.

### Usage

    import.GISTIC(
      x,
      filter.genes = NULL,
      filter.samples = NULL,
      silent = FALSE,
      trim = TRUE,
      rna.seq.data = NULL,
      rna.seq.up = NULL,
      rna.seq.down = NULL
    )

### Arguments

`x` | Either a dataframe or a filename
`filter.genes` | A list of genes
`filter.samples` | A list of samples
`silent` | A parameter to disable/enable verbose messages.
`trim` | Remove the events without occurrence
`rna.seq.data` | Either a dataframe or a filename
`rna.seq.up` | TODO
`rna.seq.down` | TODO

### Value

A TRONCO compliant representation of the input CNAs.

### Examples

    data(crc_gistic)
    gistic = import.GISTIC(crc_gistic)

[Package TRONCO version 2.26.0 Index]