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add function to parse_IUPAC_cDNA_change

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dchakro 2021-10-22 09:17:23 +03:00
parent e7ec0be360
commit 9984c87c8b
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parse_IUPAC_AAchange.R Normal file
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# 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)
parse_IUPAC_AAchange <- 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://github.com/dchakro)
# # Website: https://www.dchakro.com
# # Report issues: https://github.com/dchakro/shared_Rscripts/issues
# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE
# #<---------------------------->
# # PURPOSE:
# # For a given vector of amino acid changes like A123T, V256F, E746_A750del
# # this function returns a data frame with REF, Pos and ALT amino acids.
# # USAGE:
# # captureDF <- parse_IUPAC_AAchange(MutationColumn)
if(any(grep(pattern = "^p.",x = MutationColumn))){
MutationColumn <- gsub("p.", "", MutationColumn, fixed = T)
}
MutationColumn <- gsub("*", "X", MutationColumn, fixed = T)
AAPos <- stringi::stri_extract_first_regex(str = MutationColumn,pattern = "[0-9]+")
REF_AA <- stringi::stri_extract_first_regex(str = MutationColumn,pattern = "[ACDEFGHIKLMNPQRSTVWYX]+")
ALT_AA <- stringi::stri_extract_last_regex(str = MutationColumn,pattern = "[ACDEFGHIKLMNPQRSTVWYX]+")
return(data.frame(REF_AA,as.numeric(AAPos),ALT_AA))
}