processData: Process incoming data

In bastiaanvdroest/DriverProbabilities: Risk analysis of mutating driver genes

Description

Read the data in the given files and process it to data.frames or vector needed by downstream functions. Processing of drivers is optional, if 'process_drivers' is set to False a list of driver mutations must be given later on.

Usage

processData(mutation_rate_file, process_drivers = T,
  oncogenic_mutations_file, gene_MoA_file, prob_per_gene = F,
  trinucleotide = F, CDS_dep_invitro_file, CDS_dep_invivo_file,
  sample_celltypes_file, invivo_tissue, mut_spec_invitro_file,
  mut_spec_invivo_file)

Arguments

mutation_rate_file	Character indicating the file containing column 'Cell_type' and 'Number_of_mutations_per_cell_cycle'
oncogenic_mutations_file	Character indicating the file containing a oncogene driver catalog with columns 'gene' and 'gdna' containing the variants
gene_MoA_file	Character indicating the file containing columns 'gene' and 'gene_MoA'. The column 'gene_MoA' contains either 'Act', 'ambiguous' or 'LoF' as mode of action of gene
prob_per_gene	Boolean indicating if probability must be calculated per gene or for all genes together
trinucleotide	Boolean indicating if trinucleotide context of drivers must be computed
CDS_dep_invitro_file	Character indicating the file with the enrichment/depletion test results from the mutationalPatterns package for invitro data
CDS_dep_invivo_file	Character indicating the file with the enrichment/depletion test results from the mutationalPatterns package for invivo data
invivo_tissue	Character indicating the invivo tissue
mut_spec_invitro_file	Character indicating the file with the invitro mutational spectrum
sample_cell_type_file	Character indicating the file with the 2 colums 'Sample' and 'Type'
mut_spec_invitro_file	Character indicating the file with the invivo mutational spectrum

Value

All necessary data for processing downstream will be imported as global variables

bastiaanvdroest/DriverProbabilities documentation built on Dec. 8, 2019, 10:29 a.m.