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38 lines
No EOL
1.6 KiB
R
38 lines
No EOL
1.6 KiB
R
# Installing missing dependencies
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dependencies <- c("stringi")
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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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rm(missing_packages,dependencies)
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parse_IUPAC_AAchange <- function(MutationColumn){
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# #<---------------------------->
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# # You must include this section when:
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# # Distributing, Using and/or Modifying this code.
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# # Please read and abide by the terms of the included LICENSE.
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# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
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# #
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# # Author : Deepankar Chakroborty (https://github.com/dchakro)
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# # Website: https://www.dchakro.com
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# # Report issues: https://github.com/dchakro/shared_Rscripts/issues
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# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE
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# #<---------------------------->
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# # PURPOSE:
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# # For a given vector of amino acid changes like A123T, V256F, E746_A750del
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# # this function returns a data frame with REF, Pos and ALT amino acids.
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# # USAGE:
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# # captureDF <- parse_IUPAC_AAchange(MutationColumn)
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if(any(grep(pattern = "^p.",x = MutationColumn))){
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MutationColumn <- gsub("p.", "", MutationColumn, fixed = T)
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}
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MutationColumn <- gsub("*", "X", MutationColumn, fixed = T)
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AAPos <- stringi::stri_extract_first_regex(str = MutationColumn,pattern = "[0-9]+")
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REF_AA <- stringi::stri_extract_first_regex(str = MutationColumn,pattern = "[ACDEFGHIKLMNPQRSTVWYX]+")
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ALT_AA <- stringi::stri_extract_last_regex(str = MutationColumn,pattern = "[ACDEFGHIKLMNPQRSTVWYX]+")
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return(data.frame(REF_AA,AAPos=as.numeric(AAPos),ALT_AA))
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} |