diff --git a/CT_GA_count.R b/CT_GA_count.R
index 3522047e8f75eb3244a39188c800f135e40c4818..a76a5592010b7525be2f504d8d505633adace2cb 100644
--- a/CT_GA_count.R
+++ b/CT_GA_count.R
@@ -1,62 +1,3 @@
-
-
-CT_GA_count <- function(SampleID,Ref_Base,Alt_Base){
-# #<---------------------------->
-# # You must include this section when:
-# # Distributing, Using and/or Modifying this code.
-# # Please read and abide by the terms of the included LICENSE.
-# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
-# #
-# # Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
-# # Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
-# # License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
-# #<---------------------------->
-
-# # PURPOSE:
-# # This function takes in three vectors:
-# # SampleID = Sample IDs
-# # Ref_Base = Reference Base
-# # Alt_Base = altered base that created the mutation.
-
-# # And calculates the number of C > T and G > A changes are there (per sample)
-# # The function returns a data frame listing the number of mutations (per sample):
-# # SampleID = Sample ID
-# # Total = Total number of mutations
-# # CT = C > T changes
-# # GA = G > A changes
-# # Others = all other types of transitions and transversions combined.
-
- MutMatrix <- data.frame(SampleID,
- Ref_Base,
- Alt_Base,
- stringsAsFactors = F)
-
- return.df <- data.frame(SampleID=NA,
- Total=0,
- CT=0,
- GA=0,
- Others=0)
-
- for(SampleID in levels(MutMatrix$SampleID)){
- set <- MutMatrix[ MutMatrix$SampleID == SampleID, ]
-
- # if(dim(set)[1]==0){
- # return.df <- rbind.data.frame(return.df,c(SampleID,0,0,0,0))
- # next
- # }
-
- Total <- dim(set)[1]
-
- CT <- dim(subset(set, set$Ref_Base == "C" & set$Alt_Base == "T"))[1]
-
- GA <- dim(subset(set, set$Ref_Base == "G" & set$Alt_Base == "A"))[1]
-
- Others=Total-CT-GA
-
- return.df <- rbind.data.frame(return.df,list(SampleID,Total,CT,GA,Others),stringsAsFactors = F)
-
- Total <- 0;CT <- 0;GA <- 0;Others <- 0 # re-initialize
- rm(set)
- }
- return(return.df[-1,]) # Removes the first empty row
-}
+# Development of the script has migrated to https://github.com/dchakro/
+# replace the line sourcing this file with the following in your code.
+source('https://raw.githubusercontent.com/dchakro/shared_Rscripts/master/CT_GA_count.R')
diff --git a/IsolateCanonicalVariant.R b/IsolateCanonicalVariant.R
index 8813f2ec8c3835ee51f6d8cf8129c673179bbdd2..664134cf341e0bcb6212d065c31d0a93030637ca 100644
--- a/IsolateCanonicalVariant.R
+++ b/IsolateCanonicalVariant.R
@@ -1,127 +1,3 @@
-# Installing dependencies
-dependencies <- c("stringi", "doParallel")
-missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
-if(length(missing_packages)) install.packages(missing_packages)
-rm(missing_packages,dependencies)
-
-IsolateCanonicalVariant <- function (AAchangeAnnotations){
-# #<---------------------------->
-# # You must include this section when:
-# # Distributing, Using and/or Modifying this code.
-# # Please read and abide by the terms of the included LICENSE.
-# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
-# #
-# # Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
-# # Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
-# # License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
-# #<---------------------------->
-
-
-# # PURPOSE:
-# # From a given vector of annotations for a particular DNA change
-# # this function selects the canonical variant (if present)
-# # by cross referencing the MANE Select and RefSeq Select sets.
-
-# # LOGIC FLOW:
-# # - If there is only one annotation; that is selected
-# # - If canonical transcript is not found in MANE Select + RefSeq select
-# # or a matching transcript ID is not found in the annotation then;
-# # The mutation with to the the highest position (residue number) is selected.
-# # - If a match for canonical isoform is found then;
-# # that particular mutation is selected
-
- # importing resources
- library(doParallel)
- refseq <- readRDS(url("https://gitlab.utu.fi/deecha/shared_scripts/-/raw/master/asset/RefSeqSelect_Gene_Transcript.RDS"),"rb")
- source("https://gitlab.utu.fi/deecha/shared_scripts/-/raw/master/MutSiteFind.R")
-
- # initializing cluster
- myCluster <- makeCluster(parallel::detectCores(),
- type = "FORK",
- useXDR=F,
- .combine=cbind)
- registerDoParallel(myCluster)
- print(myCluster)
-
- file.create("log.txt")
- message(paste0("Logging processed mutations at: ",getwd(),"/log.txt"))
-
- # computation
- results <- foreach(MutInfo = AAchangeAnnotations,.combine = c) %dopar% {
- GENE <- can.isoform <- l <- l2 <- NA
- l=unique(unlist(
- stringi::stri_split_fixed(
- str = MutInfo,
- pattern = ","),
- use.names = F,
- recursive = F))
-
- if(length(l)==1){
- l2 <- unlist(stringi::stri_split_fixed(
- str = l,
- pattern = ":"),
- use.names = F,
- recursive = F)
- MUTATION <- stringi::stri_replace_first_fixed(
- str = l2[stringi::stri_detect_regex(
- str = l2,
- use.names = F,
- pattern = "^p\\.")],
- pattern = "p.",
- replacement = "")
- } else {
- GENE <- stringi::stri_sub(
- str = l[1],
- from = 1,
- to = stringi::stri_locate_first_fixed(
- str = l[1],
- pattern = ":")[,"end"]-1)
-
- can.isoform <- refseq$transcript_accession[refseq$gene_id==GENE]
-
- if(length(can.isoform)==0 | !any(stringi::stri_detect_fixed(str = l,pattern = can.isoform))){
- # Canonical isoform not found in RefSeq, or Match for Canonical isoform not found in AAchangeAnnotations
- l2 <- unlist(
- stringi::stri_split_fixed(
- str = l,
- pattern = ":"),
- use.names = F,
- recursive = F)
-
- l3 <- stringi::stri_replace_all_fixed(
- str = l2[stringi::stri_startswith_fixed(
- str = l2,
- "p.")],
- pattern = "p.",
- replacement = "")
-
- MUTATION <- l3[which.max(MutSiteFind(l3))]
- } else {
- # Canonical isoform found
- l=l[grep(can.isoform,l)]
-
- l2 <- unlist(
- stringi::stri_split_fixed(
- str = l,
- pattern = ":"),
- use.names = F,
- recursive = F)
-
- MUTATION <- stringi::stri_replace_first_fixed(
- str = l2[stringi::stri_detect_regex(
- str = l2,
- use.names = F,
- pattern = "^p\\.")],
- pattern = "p.",
- replacement = "")
- }
- }
- if(length(MUTATION)==0){
- MUTATION <- NA
- }
- cat(paste(MUTATION,"\n"),file="log.txt", append=T)
- return(MUTATION)
- }
- stopCluster(myCluster)
- return(results)
-}
+# Development of the script has migrated to https://github.com/dchakro/
+# replace the line sourcing this file with the following in your code.
+source('https://raw.githubusercontent.com/dchakro/shared_Rscripts/master/IsolateCanonicalVariant.R')
\ No newline at end of file
diff --git a/MutSiteFind.R b/MutSiteFind.R
index 70ccda65f2c48e5b0ec60b4a2d52871e21e89372..da371c902cbabbf6995e3f2d01cc2c36e80d92f5 100644
--- a/MutSiteFind.R
+++ b/MutSiteFind.R
@@ -1,31 +1,3 @@
-# Installing missing dependencies
-dependencies <- c("stringi")
-missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
-if(length(missing_packages)) install.packages(missing_packages)
-rm(missing_packages,dependencies)
-
-MutSiteFind <- function(MutationColumn){
-# #<---------------------------->
-# # You must include this section when:
-# # Distributing, Using and/or Modifying this code.
-# # Please read and abide by the terms of the included LICENSE.
-# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
-# #
-# # Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
-# # Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
-# # License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
-# #<---------------------------->
-
-
-# # PURPOSE:
-# # For a given vector of amino acid changes like A123T, V256F, E746_A750del
-# # this function returns c(123, 256, 746) as amino acid positions of
-# # the mutated residue.
-# # In case of indels, it doesn't return the range!!
-# # (i.e. returns only the start position)
-
-
- return(unlist(x = stringi::stri_extract_first_regex(str = MutationColumn,pattern = "[[:digit:]]+"), use.names = F))
-}
-
-
+# Development of the script has migrated to https://github.com/dchakro/
+# replace the line sourcing this file with the following in your code.
+source('https://raw.githubusercontent.com/dchakro/shared_Rscripts/master/MutSiteFind.R')
\ No newline at end of file
diff --git a/asset/RefSeqSelect_Gene_Transcript.RDS b/asset/RefSeqSelect_Gene_Transcript.RDS
deleted file mode 100644
index 8149ce039eaa3848159427dd3a40075c3244a06d..0000000000000000000000000000000000000000
Binary files a/asset/RefSeqSelect_Gene_Transcript.RDS and /dev/null differ
diff --git a/ggplotBreaks.R b/ggplotBreaks.R
index 48121acd46498838980ca0000b3e1b07d7eb705e..cf467944e050bb1a43449874b3c695ace75dbe7d 100644
--- a/ggplotBreaks.R
+++ b/ggplotBreaks.R
@@ -1,65 +1,3 @@
-ggplotBreaks <- function(range,tick,skip.steps=0){
-# #<---------------------------->
-# # You must include this section when:
-# # Distributing, Using and/or Modifying this code.
-# # Please read and abide by the terms of the included LICENSE.
-# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
-# #
-# # Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
-# # Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
-# # License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
-# #<---------------------------->
-
-
-# # PURPOSE:
-# # Returns a list of vectors containing breaks and labels
-# # for a continuous variable mapped to one of the axes for use with ggplot2
-# # User enters:
-# # - the range of the data
-# # - the tick amount
-# # - skip.steps (if any) = number of labels to skip
-# # (i.e. show tick but no label)
-# # e.g.
-# # ggplotBreaks(c(0,150), tick =10, skip.steps = 1) # gives
-# # $breaks
-# # 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150
-# #
-# # $labels
-# # "0" " " "20" " " "40" " " "60" " " "80" " " "100" " " "120" " " "140" " "
-
- if (length(range) != 2){
- stop("Correct format for: range = c(min_value,max_value)")
- }
- if(skip.steps<0){
- stop(" 'skip.steps' should be >= 0")
- }
- breaks <- seq(from = range[1],
- to = range[2],
- by = tick)
- if(skip.steps==0){
- labels <- as.character(breaks)
- } else {
- tmp <- c()
- labels <- unlist(
- lapply(
- breaks[seq(from = 1,
- to = length(breaks),
- by = skip.steps+1)],
- function(x) c(tmp,
- c(x,
- rep(" ",skip.steps)))),
- use.names = F)
- rm(tmp)
-
- }
- if(length(labels) < length(breaks)){
- ## Add more spaces at the end to make lengths match
- labels <- c( labels, rep(" " , (length(breaks) - length(labels))))
- }
- if ( length(breaks) < length(labels)){
- ## Remove spaces from the end to make the lengths match
- labels <- labels[1:length(breaks)]
- }
- return(list( breaks = breaks,
- labels = labels))
-}
+# Development of the script has migrated to https://github.com/dchakro/
+# replace the line sourcing this file with the following in your code.
+source('https://raw.githubusercontent.com/dchakro/shared_Rscripts/master/ggplotBreaks.R')
\ No newline at end of file
diff --git a/unparalogMutations.R b/unparalogMutations.R
index ddf3ff588b21dacb4ff7dc58713e11ada0c44339..d99f32079bb793f871d3c86558d1793a1a4d0047 100644
--- a/unparalogMutations.R
+++ b/unparalogMutations.R
@@ -1,92 +1,3 @@
-# Installing missing dependencies
-dependencies <- c("stringi", "progress")
-missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
-if(length(missing_packages)) install.packages(missing_packages)
-rm(missing_packages,dependencies)
-
-unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", GeneColName , AnnotationColName ){
-# #<---------------------------->
-# # You must include this section when:
-# # Distributing, Using and/or Modifying this code.
-# # Please read and abide by the terms of the included LICENSE.
-# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
-# #
-# # Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
-# # Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
-# # License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
-# #<---------------------------->
-
-
-# # PURPOSE:
-# # In the gene column in your SNV annotation if you see something like:
-# # e.g. PRAMEF7;PRAMEF8 OR PRAMEF7,PRAMEF8
-# # then your mutations annotations have gene paralogs.
-# # This script aims to de-couple those paralogs into individual their rows.
-# #
-
-# # INFO on what to pass as the function parameters:
-# Assign correct paralog_separator found in the gene column of your SNV annotations # e.g. if the Gene column has entries like PRAMEF7;PRAMEF8
-# then the paralog_separator is ";"
-# or set it to whatever separator is used by your SNV annotation software.
-
-# Assign correct annotation_separator in the Amino acid change column of your SNV annotations
-# "PRAMEF8:NM_001012276:exon3:c.C541A:p.Q181K,PRAMEF7:NM_001012277:exon3:c.C541A:p.Q181K"
-# In the above example the annotation_separator is ","
-
-# GeneColName = Column name in the SNV annotation table where the Genes are listed
-
-# AnnotationColName = Column name in the SNV annotation table where the Amino acid changes are listed
-
-# <--------------->
-
- # Sanity checks
- check_paralog_sep <- !any(stringi::stri_detect_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
- check_annotation_sep <- !any(stringi::stri_detect_fixed(str = DATA$AAChange.refGene, pattern = annotation_separator))
-
- idx_Gene <- which(colnames(DATA) == GeneColName)
- idx_Annotation <- which(colnames(DATA) == AnnotationColName)
-
- if(length(idx_Gene) == 0 | length(idx_Annotation) == 0 | check_paralog_sep | check_annotation_sep) {
- message(stringi::stri_c("You entered :-->",
- "\nparalog_separator = ",paralog_separator,
- "\nannotation_separator = ",annotation_separator,
- "\nGeneColName = ", GeneColName,
- "\nAnnotationColName = ",AnnotationColName))
- stop("Inconsistencies with these input parameters.\n Ensure they are correct and try again.")
- }
- # Cleanup
- rm(check_paralog_sep,check_annotation_sep)
- gc()
-
- current.idx <- 1 # nrow(DATA)+1
- paralog.idx <- which(stringi::stri_detect_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
- pb <- progress::progress_bar$new(total=length(paralog.idx),format = " [:bar] :current/:total (:percent)",); pb$tick(0)
-
- Number_of_paralogs <- sum(stringi::stri_count_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
- message(stringi::stri_c("There are ",length(paralog.idx)," annotations with ", Number_of_paralogs," paralogs."))
-
- # copying structure of original DATA
- DATA.new <- DATA[1,]; DATA.new <- DATA.new[-1,]
-
- # Creating empty table which will be populated in the for loop
- DATA.new <- dplyr::bind_rows(DATA.new,data.frame(matrix(nrow = (length(paralog.idx)+Number_of_paralogs), ncol = ncol(DATA),dimnames = list(c(),colnames(DATA))),stringsAsFactors = F))
-
- # Beginning isolation of the paralogs
- for(i in paralog.idx){
- Muts <- unlist(stringi::stri_split_fixed(DATA$AAChange.refGene[i],annotation_separator),use.names = F,recursive = F)
- for (gene in unlist(stringi::stri_split_fixed(DATA$Gene.refGene[i],pattern = paralog_separator),use.names = F,recursive = F)){
- DATA.new[current.idx,] <- DATA[i,]
- DATA.new$Gene.refGene[current.idx] <- gene
- DATA.new$AAChange.refGene[current.idx] <- paste0(Muts[grep(gene,Muts,fixed = T)],collapse=annotation_separator)
- current.idx <- current.idx+1
- }
- pb$tick(1)
- }
- # removing the original rows with the paralogs as they are all unparalogged now
- DATA <- DATA[-paralog.idx,]
- DATA <- dplyr::bind_rows(DATA,DATA.new)
- rm(DATA.new) ; gc()
-
- rownames(DATA) <- as.character(seq(1,length(DATA[,1])))
- return (DATA)
-}
+# Development of the script has migrated to https://github.com/dchakro/
+# replace the line sourcing this file with the following in your code.
+source('https://raw.githubusercontent.com/dchakro/shared_Rscripts/master/unparalogMutations.R')
\ No newline at end of file