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https://github.com/dchakro/shared_Rscripts.git
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99a6589b9b
unparalogMutations checks & installs dependencies only when it is sourced, and not everytime the function was called (as previously).
31 lines
1.2 KiB
R
31 lines
1.2 KiB
R
# #<---------------------------->
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# # Please include this section when distributing and/or using this code.
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# # Please read and abide by the terms of the included LICENSE
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# #
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# # Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
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# # Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
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# # License: https://gitlab.utu.fi/deecha/shared_scripts/-/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 c(123, 256, 746) as amino acid positions of
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# # the mutated residue.
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# # In case of indels, it doesn't return the range!! (returns only the start position)
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# #
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# #<---------------------------->
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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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## ----- Legacy version relying on r::base --------
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MutSiteFind.legacy=function(MutationColumn){
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MutationSite=c()
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for(i in seq(1:length(MutationColumn))){
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Site=regmatches(MutationColumn[i], gregexpr("[[:digit:]]+",MutationColumn[i]))[[1]][1]
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MutationSite=c(MutationSite,Site)
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}
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return(MutationSite)
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}
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