importM.COSMIC: Import mutation data from a COSMIC database.

In hyginn/rete: Network Analysis for Cell- and Systems Biology

Description

importM.COSMIC Imports a tsv file containing CNA data from COSMIC. Imports a TSV file mapping COSMIC gene IDs to HGNC gene symbols, required to match a CNA gene symbol to an HGNC gene symbol (replaced by calls to fastMap()). Returns an rCNA object in an RDS, where column names represents samples (as TCGA-SampleID (note that the required information for a proper TCGA mutation barcode is not available for COSMIC data, and that the sampleID for this data is specific to COSMIC data)), row names are HGNC gene symbols, and the values represent copy number.

Usage

importM.COSMIC(fNameCNA, outFName, silent = FALSE, writeLog = TRUE)

Arguments

fNameCNA	The path to a TSV file with CNA data from COSMIC.
outFName	The path to an output file for the rCNA RDS object.
silent	Controls whether output to console should be suppressed. FALSE by default.
writeLog	Controls whether writing the result to the global logfile is enabled. TRUE by default.

Value

Return rCNA object of COSMIC CNA data as RDS compressed data frame file.

COSMIC CNA

The format of the COSMIC CNA data is as follows. (through sftp, run get with this path: /files/grch38/cosmic/v80/CosmicCompleteCNA.tsv.gz)

[col number] Heading [1] CNA_ID [2] Gene ID [3] Gene Name [4] Sample ID [5] Tumour ID [6] Primary Site [7-9] Site Subtype 1-3 [10] Primary Histology [11-13] Histology Subtype 1-3 [14] Sample Name [15] Total Copy Number [16] Minor Allele CN [17] Mutation Type [18] Study ID [19] GRCh Coordinate System [20] Genomic Coordinates of Variation

Examples

## Not run: 
fNameCNA <- "./../test/COSMIC/testCosmicCNA.tsv"
outFName <- "cosmicCNA.rds"

importM.COSMIC(fNameCNA,
               outFName,
               silent = TRUE,
               writeLog = FALSE)

## End(Not run)

hyginn/rete documentation built on May 17, 2019, 9:16 p.m.