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85 lines
4.3 KiB
R
85 lines
4.3 KiB
R
# #<---------------------------->
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# # Author : Deepankar Chakroborty
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# # URL: https://gitlab.utu.fi/deecha
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# # Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
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# # Please include this when distributing my code.
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# # In the gene column in your SNV annotation if you see something like:
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# # e.g. PRAMEF7;PRAMEF8 OR PRAMEF7,PRAMEF8
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# # then your mutations annotations have gene paralogs.
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# #
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# # This script aims to de-couple those paralogs into individual their rows.
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# #
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# #<---------------------------->
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### Info:
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# Assign correct paralog_separator found in the gene column of your SNV annotations # e.g. if the Gene column has entries like PRAMEF7;PRAMEF8
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# then the paralog_separator is ";"
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# or set it to whatever separator is used by your SNV annotation software.
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# Assign correct annotation_separator in the Amino acid change column of your SNV annotations
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# "PRAMEF8:NM_001012276:exon3:c.C541A:p.Q181K,PRAMEF7:NM_001012277:exon3:c.C541A:p.Q181K"
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# In the above example the annotation_separator is ","
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# GeneColName = Column name in the SNV annotation table where the Genes are listed
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# AnnotationColName = Column name in the SNV annotation table where the Amino acid changes are listed
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# <--------------->
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unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", GeneColName , AnnotationColName ){
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# Installing missing dependencies
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dependencies <- c("stringi", "progress")
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missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
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if(length(missing_packages)) install.packages(missing_packages)
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# Sanity checks
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check_paralog_sep <- !any(stringi::stri_detect_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
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check_annotation_sep <- !any(stringi::stri_detect_fixed(str = DATA$AAChange.refGene, pattern = annotation_separator))
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idx_Gene <- which(colnames(DATA) == GeneColName)
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idx_Annotation <- which(colnames(DATA) == AnnotationColName)
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if(length(idx_Gene) == 0 | length(idx_Annotation) == 0 | check_paralog_sep | check_annotation_sep) {
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message(stringi::stri_c("You entered :-->",
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"\nparalog_separator = ",paralog_separator,
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"\nannotation_separator = ",annotation_separator,
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"\nGeneColName = ", GeneColName,
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"\nAnnotationColName = ",AnnotationColName))
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stop("Inconsistencies with these input parameters.\n Ensure they are correct and try again.")
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}
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# Cleanup
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rm(missing_packages,dependencies,check_paralog_sep,check_annotation_sep)
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gc()
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current.idx <- nrow(DATA)+1
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paralog.idx <- which(stringi::stri_detect_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
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pb <- progress::progress_bar$new(total=length(paralog.idx),format = " [:bar] :current/:total (:percent)",); pb$tick(0)
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Number_of_paralogs <- sum(stringi::stri_count_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
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message(stringi::stri_c("There are ",length(paralog.idx)," annotations with ", Number_of_paralogs," paralogs."))
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# copying structure of original DATA
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DATA.add <- DATA[1,]; DATA.add <- DATA.add[-1,]
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# Adding the empty rows to original table.
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# These rows will be populated in the for loop
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DATA.add <- dplyr::bind_rows(DATA.add,data.frame(matrix(nrow = (length(paralog.idx)+Number_of_paralogs), ncol = ncol(DATA),dimnames = list(c(),colnames(DATA))),stringsAsFactors = F))
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DATA <- dplyr::bind_rows(DATA,DATA.add)
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rm(DATA.add) ; gc()
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# Beginning isolation of the paralogs
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for(i in paralog.idx){
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Muts <- unlist(stringi::stri_split_fixed(DATA$AAChange.refGene[i],annotation_separator),use.names = F,recursive = F)
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for (gene in unlist(stringi::stri_split_fixed(DATA$Gene.refGene[i],pattern = paralog_separator),use.names = F,recursive = F)){
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DATA[current.idx,] <- DATA[i,]
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DATA$Gene.refGene[current.idx] <- gene
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DATA$AAChange.refGene[current.idx] <- paste0(Muts[grep(gene,Muts,fixed = T)],collapse=",")
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current.idx <- current.idx+1
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}
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pb$tick(1)
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}
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# removing the original rows with the paralogs as they are all unparalogged now
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DATA <- DATA[-paralog.idx,]
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rownames(DATA) <- as.character(seq(1,length(DATA[,1])))
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return (DATA)
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}
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