create_mutation_catalogue_from_VR {YAPSA} | R Documentation

## Create a Mutational Catalogue from a VRanges Object

### Description

This function creates a mutational catalogue from a VRanges Object by first calling `mutationContext` to establish the motif context of the variants in the input VRanges and then calling `motifMatrix` to build the mutational catalogue `V`.

### Usage

    create_mutation_catalogue_from_VR(
      in_vr,
      in_refGenome,
      in_wordLength,
      in_PID.field = "PID",
      in_verbose = 0,
      in_rownames = c(),
      adapt_rownames = 1
    )

### Arguments

`in_vr` | A VRanges object 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.
`in_refGenome` | The reference genome handed over to `mutationContext` and used to extract the motif context of the variants in `in_vr`.
`in_wordLength` | The size of the motifs to be extracted by `mutationContext`
`in_PID.field` | Indicates the name of the column in which the PID (patient or sample identifier) is encoded
`in_verbose` | Verbose if `in_verbose=1`
`in_rownames` | Optional parameter to specify rownames of the mutational catalogue `V` i.e. the names of the features.
`adapt_rownames` | Rownames of the output `matrix` will be adapted if `adapt_rownames=1`

### Value

A list with entries `matrix`, `frame`,

- `matrix`: The mutational catalogue `V`

- `frame`: Additional and meta information on rownames (features), colnames (PIDs) and subgroup attribution.

### See Also

`mutationContext`

`motifMatrix`

### Examples

     library(BSgenome.Hsapiens.UCSC.hg19)
     data(lymphoma_test)
     data(sigs)
     word_length <- 3
     temp_vr <- makeVRangesFromDataFrame(
       lymphoma_test_df,in_seqnames.field="CHROM",
       in_subgroup.field="SUBGROUP",verbose_flag=1)
     temp_list <- create_mutation_catalogue_from_VR(
       temp_vr,in_refGenome=BSgenome.Hsapiens.UCSC.hg19,
       in_wordLength=word_length,in_PID.field="PID",
       in_verbose=1)
     dim(temp_list$matrix)
     head(temp_list$matrix)
     test_list <- split(lymphoma_test_df,f=lymphoma_test_df$PID)
     other_list <- list()
     for(i in seq_len(length(test_list))){
       other_list[[i]] <- test_list[[i]][c(1:80),]
     }
     other_df <- do.call(rbind,other_list)
     other_vr <- makeVRangesFromDataFrame(
       other_df,in_seqnames.field="CHROM",
       in_subgroup.field="SUBGROUP",verbose_flag=1)
     other_list <- create_mutation_catalogue_from_VR(
       other_vr,in_refGenome=BSgenome.Hsapiens.UCSC.hg19,
       in_wordLength=word_length,in_PID.field="PID",
       in_verbose=1,in_rownames=rownames(AlexCosmicValid_sig_df))
     dim(other_list$matrix)
     head(other_list$matrix)

[Package YAPSA version 1.20.1 Index]