Error while extracting pseudo amino acid composition using protr
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, the .txt file has 119 fasta sequences
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