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Question: Error while extracting pseudo amino acid composition using protr
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gravatar for shreyasarkar0
7 days ago by
shreyasarkar00 wrote:

I'm trying to extract the pseudo amino acid composition using the protr package but I'm getting the error. here is the code :

source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")
library(protr)
testNeg_seq= readFASTA("C:/Users/Shreya Sarkar/Desktop/negativeboth.txt")
####check if there are 20 aa in all the seq 
check1_test = t(lapply(testNeg_seq, protcheck))
length(check1_test)
#####check if there are 20 aa in all the seq and remove the rest
check2_test = testNeg_seq[(sapply(testNeg_seq, protcheck))]
length(check2_test)
######gives pseudo amino acid Compostion
pseudo1 = t(lapply(check2_test, extractPAAC))
pseudo1
#gives amino acid composition
aminoAcid_testNeg = t(lapply(check2_test, extractAAC))
aminoAcid_testNeg

error is:

Error in FUN(X[[i]], ...) : Length of the protein sequence must be greater than "lambda"

the Amino Acid function is working but PAAC function is not working , the .txt file has 119 fasta sequences. 

please help me 

 

ADD COMMENTlink written 7 days ago by shreyasarkar00
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