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Annovar functions

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dchakro 2020-12-16 19:45:17 +02:00
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Annovar/AnnovarMutCodeFind.R Normal file
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annovarMutCodeFind=function(MutationColumn,isoform){
# #<---------------------------->
# # 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:
# # This function takes a mutation info column from ANNOVAR output
# # and selects the protein change based on the isoform provided.
# # More about annovar: https://en.wikipedia.org/wiki/ANNOVAR
# # INPUT:
# # MutationColumn = Mutation column from ANNOVAR output
# # (usually called: "AAChange.refGene")
# # isoform = the GenBank Identifier, you can find it from the the ANNOVAR mutation info column.
# # Default Isoform codes:
# # EGFR = NM_005228
# # ERBB2 = NM_004448
# # ERBB3 = NM_001982
# # ERBB4 (Jm-A, Cyt-1) = NM_005235
# # ERBB4 (Jm-A, Cyt-2) = NM_001042599
# # Example usage:
# # annovarMutCodeFind(MutationColumn = yourData$AAChange.refGene,
# # isoform = "NM_005228")
MutationList=c("List of mutations")
for(i in seq(1:length(MutationColumn))){
MutInfo=MutationColumn[i]
l=sort(unique(unlist(strsplit(MutInfo,","))))
l2=l[grep(isoform,l)]
l2.s=unique(unlist(strsplit(l2,":")))
l3=l2.s[grep("^p",l2.s)]
l3=gsub("p.","",l3)
l3=gsub("X","*",l3)
MUTATION=l3
if(length(MUTATION)==0) MUTATION=" "
MutationList=c(MutationList,MUTATION)
}
return(MutationList[-1])
}
annovarMutCodeFind(MutationColumn = Mutation.Table$AAChange.refGene,isoform = "NM_001982")

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