I have a table of protein data that looks like this:
ASV1 K L A G G S A Q A I K M P A A Q
ASV4 K L A G G S A Q A I K M P A D Q
ASV3 K L A G G S A Q A I K M P A A Q
ASV2 K L A G G S A Q S I K M P A N Q
ASV5 K L A G G S A Q A I K M P A A Q
I want to convert this table into a binary form, where the common/usual amino acid at each site is represented by 1 and the other/less common variants are represented by -1, like this:
ASV1 1 1 1 1 1 1 1 1 1 1 1
ASV4 -1 1 1 1 1 1 -1 1 1 1 1
ASV3 1 1 1 1 1 1 -1 1 1 1 1
ASV2 1 1 -1 1 1 1 1 1 1 1 1
ASV5 1 1 1 1 1 -1 1 1 1 -1 1
Is there any way to do this in R?
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written
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pearl2070 •
Edited 2023-01-16 Not sure if there is any but the following function should work:
binaryVar = function(vR, vV){ #vR: the ref string, vV: the variant string
vRef = unlist(strsplit(vR, " ")) #Spliting string to its elements
vVariant = unlist(strsplit(vV, " ")) #Spliting string to its elements
element_count = length(vRef) # function assumes both vRef and vVariant have the same length
binary <- c()
for(index in 1:element_count){
binary[index] = ifelse(vRef[index] == vVariant[index], "1", "-1")
}
return(binary)
}
#Test
ASV1 = c('K L A G G S A Q A I K M P A A Q')
ASV4 = c('K L A G G S A Q A I K M P A D Q')
asv4_binary = binaryVar(ASV1, ASV4)
asv4_binary
[1] "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "-1" "1"
If you have a data frame, you may use this function and iterate over the rows and record the output for each iteration into a new list, then convert the list to a data frame.
Thanks! But the test is returning an error when I run it:
asv4_binary = binaryVar(ASV1, ASV4)
Error in binaryVar(ASV1, ASV4) : object 'binary' not found
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written
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pearl2070 •
Ops! just updated the function and now it should work. The issue was because of not having defined 'binary' variable before running the loop.
It works now, thank you!
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Can you explain your example more? For example, why -1 is in the first position of ASV4?
My mistake, I didn't base the example binary pattern of the ASVs on the example sequence data when typing them out, so they don't match up.
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