dot-mutations_gene_binary: Make Binary Matrix From Mutation data frame
In AxelitoMartin/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data

.mutations_gene_binary

R Documentation

Make Binary Matrix From Mutation data frame

Make Binary Matrix From Mutation data frame

.mutations_gene_binary(
  mutation,
  samples,
  mut_type,
  snp_only,
  include_silent,
  specify_panel,
  names_mut_dict
)

`mutation`	A data frame of mutations in the format of a maf file.
`samples`	a character vector specifying which samples should be included in the resulting data frame. Default is NULL is which case all samples with an alteration in the mutation, cna or fusions file will be used. If you specify a vector of samples that contain samples not in any of the passed genomic data frames, 0's (or NAs when appropriate if specifying a panel) will be returned for every column of that patient row.
`mut_type`	The mutation type to be used. Options are "omit_germline", "somatic_only", "germline_only" or "all". Note "all" will keep all mutations regardless of status (not recommended). Default is omit_germline which includes all somatic mutations, as well as any unknown mutation types (most of which are usually somatic)
`snp_only`	Boolean to rather the genetics events to be kept only to be SNPs (insertions and deletions will be removed). Default is FALSE.
`include_silent`	Boolean to keep or remove all silent mutations. TRUE keeps, FALSE removes. Default is FALSE.
`specify_panel`	Default is `"no"` where no panel annotation is done. Otherwise pass a character vector of length 1 with a panel id (see `gnomeR::gene_panels` for available panels), or `"impact"` for automated IMPACT annotation. Alternatively, you may pass a data frame of `sample_id`-`panel_id` pairs specifying panels for each sample for which to insert NAs indicating genes not tested. See below for details.