import.GISTIC {TRONCO} | R Documentation |
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.
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 )
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 |
A TRONCO compliant representation of the input CNAs.
gistic = import.GISTIC(crc_gistic)