mutsigcl_global: Permutation-based identification of hotspot-enriched genes...
In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description Usage Arguments See Also Examples

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

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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)

`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.

mutsig.gene,mutsig.pathway,mutsigclfn

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)