tomaftools: tomaftools

In likelet/CaMutQC: An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

tomaftools

Description

Transform a CaMutQC maf object to a maftools maf object.

Usage

tomaftools(
  maf,
  clinicalData = NULL,
  rmFlags = FALSE,
  removeDuplicatedVariants = TRUE,
  useAll = TRUE,
  gisticAllLesionsFile = NULL,
  gisticAmpGenesFile = NULL,
  gisticDelGenesFile = NULL,
  gisticScoresFile = NULL,
  cnLevel = "all",
  cnTable = NULL,
  isTCGA = FALSE,
  vc_nonSyn = NULL,
  verbose = TRUE
)

Arguments

maf	An MAF data frame, generated by vcfToMAF function.
clinicalData	Clinical data associated with each # sample/Tumor_Sample_Barcode in MAF. Could be a text file or a data.frame. Default NULL. Inherited from maftools.
rmFlags	Default FALSE. Can be TRUE or an integer. If TRUE, removes all the top 20 FLAG genes. If integer, remove top n FLAG genes. Inherited from maftools.
removeDuplicatedVariants	removes repeated variants in a particuar sample, mapped to multiple transcripts of same Gene. See Description. Default TRUE. Inherited from maftools.
useAll	logical. Whether to use all variants irrespective of values in Mutation_Status. Defaults to TRUE. If FALSE, only uses with values Somatic. Inherited from maftools.
gisticAllLesionsFile	All Lesions file generated by gistic. e.g; all_lesions.conf_XX.txt, where XX is the confidence level. Default NULL. Inherited from maftools.
gisticAmpGenesFile	Amplification Genes file generated by gistic. e.g; amp_genes.conf_XX.txt, where XX is the confidence level. Default NULL. Inherited from maftools.
gisticDelGenesFile	Deletion Genes file generated by gistic. e.g; del_genes.conf_XX.txt, where XX is the confidence level. Default NULL. Inherited from maftools.
gisticScoresFile	scores.gistic file generated by gistic. Default NULL Inherited from maftools.
cnLevel	level of CN changes to use. Can be 'all', 'deep' or 'shallow'. Default uses all i.e, genes with both 'shallow' or 'deep' CN changes. Inherited from maftools.
cnTable	Custom copynumber data if gistic results are not available. Input file or a data.frame should contain three columns in aforementioned order with gene name, Sample name and copy number status (either 'Amp' or 'Del'). Default NULL. Inherited from maftools.
isTCGA	Is input MAF file from TCGA source. If TRUE uses only first 12 characters from Tumor_Sample_Barcode. Inherited from maftools.
vc_nonSyn	NULL. Provide manual list of variant classifications to be considered as non-synonymous. Rest will be considered as silent variants. Default uses Variant Classifications with High/Moderate variant consequences. Inherited from maftools.
verbose	TRUE logical. Default to be talkative and prints summary. Inherited from maftools.

Value

An maf object that can be recognized by maftools.

Examples

maf_CaMutQC <- vcfToMAF(system.file("extdata/Multi-caller/",
package="CaMutQC"), multiVCF=TRUE)
maf_maftools <- tomaftools(maf_CaMutQC)

likelet/CaMutQC documentation built on Aug. 17, 2024, 4 a.m.