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

gistic = import.GISTIC(crc_gistic)


[Package TRONCO version 2.16.2 Index]