sequence - A for loop with strsplit in R error -
i'd preface post new r , bioinformatics coding, , i'd appreciate input knowledgable community. goal code posted below generate pie charts show amino acid abundance per protein blast results. uploaded csv file uniprot, converted matrix, , wrote out code below. keep getting error: in aas[i] = table(strsplit(blast_aa_seqs[i], "", usebytes = true)) :number of items replace not multiple of replacement length. column 8 output column contains amino acid sequences. in advance!
mydata=read.table("cdpkbeta_blast_results.csv",header=true,sep=",") mydata=as.matrix(mydata) aas=c() blast_aa_seqs=c() for(i in 1:nrow(mydata)){ print(i) blast_aa_seqs[i]=mydata[i,8] aas[i]=table(strsplit(blast_aa_seqs[i],"", usebytes=true)) pie(aas, col=rainbow(length(aas)), main="residue abundance") }
lal<-c() lal[1]=table(strsplit("", "", usebytes = t))
empty string problem (blast_aa_seqs[i] empty string)
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