tomaftools: tomaftools

View source: R/tomaftools.R

tomaftoolsR Documentation

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.