create_mutation_catalogue_from_df: Create a Mutational Catalogue from a data frame
In slw287r/yapsa: Yet Another Package for Signature Analysis

Description Usage Arguments Value See Also Examples

This function creates a mutational catalogue from a data frame. It is a wrapper function for create_mutation_catalogue_from_VR: it first creates a VRanges object from the data frame by makeVRangesFromDataFrame and then passes this object on to the above mentioned custom function.

create_mutation_catalogue_from_df(
  this_df,
  this_refGenome_Seqinfo = NULL,
  this_seqnames.field = "X.CHROM",
  this_start.field = "POS",
  this_end.field = "POS",
  this_PID.field = "PID",
  this_subgroup.field = "subgroup",
  this_refGenome,
  this_wordLength,
  this_verbose = 1,
  this_rownames = c(),
  this_adapt_rownames = 1
)

`this_df`	A data frame constructed from a vcf-like file of a whole cohort. The first columns are those of a standard vcf file, followed by an arbitrary number of custom or used defined columns. One of these can carry a PID (patient or sample identifyier) and one can carry subgroup information.
`this_refGenome_Seqinfo`	A seqInfo object, referring to the reference genome used. Argument passed on to `makeGRangesFromDataFrame` and thus indirectly to `makeGRangesFromDataFrame`.
`this_seqnames.field`	Indicates the name of the column in which the chromosome is encoded
`this_start.field`	Indicates the name of the column in which the start coordinate is encoded
`this_end.field`	Indicates the name of the column in which the end coordinate is encoded
`this_PID.field`	Indicates the name of the column in which the PID (patient or sample identifier) is encoded
`this_subgroup.field`	Indicates the name of the column in which the subgroup information is encoded
`this_refGenome`	The reference genome handed over to `create_mutation_catalogue_from_VR` and indirectly to `mutationContext` and used to extract the motif context of the variants in `in_vr`.
`this_wordLength`	The size of the motifs to be extracted by `mutationContext`
`this_verbose`	Verbose if `this_verbose=1`
`this_rownames`	Optional parameter to specify rownames of the mutational catalogue `V` i.e. the names of the features.
`this_adapt_rownames`	Rownames of the output `matrix` will be adapted if `this_adapt_rownames=1`

A list with entries matrix and frame obtained from create_mutation_catalogue_from_VR:

matrix: The mutational catalogue V
frame: Additional and meta information on rownames (features), colnames (PIDs) and subgroup attribution.

makeVRangesFromDataFrame

create_mutation_catalogue_from_VR

 library(BSgenome.Hsapiens.UCSC.hg19)
 data(lymphoma_test)
 word_length <- 3
 temp_list <- create_mutation_catalogue_from_df(
   lymphoma_test_df,this_seqnames.field = "CHROM",
   this_start.field = "POS",this_end.field = "POS",
   this_PID.field = "PID",this_subgroup.field = "SUBGROUP",
   this_refGenome = BSgenome.Hsapiens.UCSC.hg19,
   this_wordLength = word_length)
   dim(temp_list$matrix)
   head(temp_list$matrix)