| aa9212ce |
GPo_of_hotspots <- function(hotspot_mutations){
|
| 8f5081c0 |
hotspot_mutations$AA_position <- paste(hotspot_mutations$Ensembl_id, "-",
hotspot_mutations$Prot_position,
sep = "")
|
| aa9212ce |
TestData$AA_position <- paste(TestData$Ensembl_gene_id, "-",
TestData$Protein_residue, sep = "")
|
| 8f5081c0 |
cols_of_interest <- c("Genomic_coordinate", "Original_base",
"Mutated_base", "AA_position")
|
| aa9212ce |
hotspots_genomic_info <- unique(TestData[TestData$AA_position %in%
|
| 8f5081c0 |
hotspot_mutations$AA_position,
cols_of_interest])
|
| aa9212ce |
coordinates_sep <- data.frame(do.call('rbind',
strsplit(as.character(hotspots_genomic_info$Genomic_coordinate),
':',fixed=TRUE)))
prot_residue_info <- data.frame(do.call('rbind',
strsplit(as.character(hotspots_genomic_info$AA_position),
'-',fixed=TRUE)))
|
| b430497f |
chr_info = paste("chr", coordinates_sep$X1)
position_on_chr = coordinates_sep$X2
hotspots_GPo <- GPos(seqnames=chr_info, pos= position_on_chr, stitch=FALSE)
|
| aa9212ce |
GenomicRanges::mcols(hotspots_GPo)$REF_NT <- as.character(hotspots_genomic_info$Original_base)
GenomicRanges::mcols(hotspots_GPo)$MUT_NT <- as.character(hotspots_genomic_info$Mutated_base)
GenomicRanges::mcols(hotspots_GPo)$Gene_ID <- as.character(prot_residue_info$X1)
GenomicRanges::mcols(hotspots_GPo)$Protein_pos <- as.character(prot_residue_info$X2)
return(hotspots_GPo)
}
|
