create_mutation_catalogue_from_df: Create a Mutational Catalogue from a data frame

In YAPSA: Yet Another Package for Signature Analysis

Description

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.

Usage

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
)

Arguments

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

Value

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.

See Also

makeVRangesFromDataFrame

create_mutation_catalogue_from_VR

Examples

 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)

YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.