import.GISTIC: import.GISTIC

In TRONCO: TRONCO, an R package for TRanslational ONCOlogy

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)

TRONCO documentation built on Nov. 8, 2020, 5:51 p.m.