create_mutation_catalogue_from_VR {YAPSA} | R Documentation |
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
.
create_mutation_catalogue_from_VR(in_vr, in_refGenome, in_wordLength, in_PID.field = "PID", in_verbose = 0, in_rownames = c(), adapt_rownames = 1)
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
|
in_wordLength |
The size of the motifs to be extracted by
|
in_PID.field |
Indicates the name of the column in which the PID (patient or sample identifier) is encoded |
in_verbose |
Verbose if |
in_rownames |
Optional parameter to specify rownames of the mutational catalogue |
adapt_rownames |
Rownames of the output |
A list with entries
matrix
,
frame
,
matrix
:
The mutational catalogue V
frame
:
Additional and meta information on rownames (features), colnames (PIDs)
and subgroup attribution.
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)