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48 lines
1.7 KiB
R
48 lines
1.7 KiB
R
annovar_cDNA_Find=function(MutationColumn,isoform){
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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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# # This function takes a mutation info column from ANNOVAR output
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# # and selects the cDNA change based on the isoform provided.
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# # More about annovar: https://en.wikipedia.org/wiki/ANNOVAR
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# # INPUT:
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# # MutationColumn = Mutation column from ANNOVAR output
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# # (usually called: "AAChange.refGene")
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# # isoform = the GenBank Identifier, you can find it from the the ANNOVAR mutation info column.
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# # Default Isoform codes:
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# # EGFR = NM_005228
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# # ERBB2 = NM_004448
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# # ERBB3 = NM_001982
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# # ERBB4 (Jm-A, Cyt-1) = NM_005235
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# # ERBB4 (Jm-A, Cyt-2) = NM_001042599
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# # Example usage:
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# # annovar_cDNA_Find(MutationColumn = yourData$AAChange.refGene,
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# # isoform = "NM_005228")
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MutationList=c("List of mutations")
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for(i in seq(1:length(MutationColumn))){
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MutInfo=MutationColumn[i]
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l=sort(unique(unlist(strsplit(MutInfo,","))))
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l2=l[grep(isoform,l)]
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l2.s=unique(unlist(strsplit(l2,":")))
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l3=l2.s[grep("^c",l2.s)]
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l3=gsub("c.","",l3)
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#l3=gsub("X","*",l3)
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MUTATION=l3
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if(length(MUTATION)==0) MUTATION=" "
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MutationList=c(MutationList,MUTATION)
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}
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return(MutationList[-1])
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}
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