mutsigcl_global: Permutation-based identification of hotspot-enriched genes...

Description Usage Arguments See Also Examples

View source: R/mutsigcl_global.R

Description

Permutation-based identification of hotspot-enriched genes without taking into account mutational contexts.

Usage

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mutsigcl_global(Oncotator_file, NCBI_CCDS_GeneID2CDS_Positions_Rdata_file, d=NULL, NCBI_CCDS_GeneID2CDS_Positions=NULL, nperm=20000, outfile='mutsigcl_global_output.txt', exclude_indel=TRUE)
generate_mutsigcl_global_bkgr_info(CCDS_current_file)

Arguments

Oncotator_file

Oncotator annotated file.

NCBI_CCDS_GeneID2CDS_Positions_Rdata_file

Gene info derived from CCDS.current.txt, obtained from ftp.ncbi.nlm.nih.gov/pub/CCDS/archive/Hs37.3/.

d

A data frame refers to Oncotator_file.

NCBI_CCDS_GeneID2CDS_Positions

The R object stored in NCBI_CCDS_GeneID2CDS_Positions_Rdata_file, obtained from generate_mutsigcl_global_bkgr_info(...).

nperm

Number of permutation.

outfile

Output file.

exclude_indel

If TRUE exclude indels.

See Also

mutsig.gene,mutsig.pathway,mutsigclfn

Examples

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library(parallel)
library(fastcluster) # accelerate MutSigCL analysis
options(mc.cores=4)  # Use 4 cores in permutation.

# NCBI_CCDS_GeneID2CDS_Positions <- generate_mutsigcl_global_bkgr_info("CCDS.current.txt") ## Generate bkgr info for CCDS genes if required
NCBI_CCDS_GeneID2CDS_Positions_Rdata_file="/ifshk1/BC_CANCER/03user/lixiangchun/iCGA/v0.02/NCBI_CCDS_GeneID2CDS_Positions.RData"
# mutsigcl_global("exomic.maf", NCBI_CCDS_GeneID2CDS_Positions_Rdata_file)

lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.