x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
# using five customized amino acid property classification
group1 <- list(
"hydrophobicity" = c("R", "K", "E", "D", "Q", "N"),
"normwaalsvolume" = c("G", "A", "S", "T", "P", "D", "C"),
"polarizability" = c("G", "A", "S", "D", "T"),
"secondarystruct" = c("E", "A", "L", "M", "Q", "K", "R", "H"),
"solventaccess" = c("A", "L", "F", "C", "G", "I", "V", "W")
)
group2 <- list(
"hydrophobicity" = c("G", "A", "S", "T", "P", "H", "Y"),
"normwaalsvolume" = c("N", "V", "E", "Q", "I", "L"),
"polarizability" = c("C", "P", "N", "V", "E", "Q", "I", "L"),
"secondarystruct" = c("V", "I", "Y", "C", "W", "F", "T"),
"solventaccess" = c("R", "K", "Q", "E", "N", "D")
)
group3 <- list(
"hydrophobicity" = c("C", "L", "V", "I", "M", "F", "W"),
"normwaalsvolume" = c("M", "H", "K", "F", "R", "Y", "W"),
"polarizability" = c("K", "M", "H", "F", "R", "Y", "W"),
"secondarystruct" = c("G", "N", "P", "S", "D"),
"solventaccess" = c("M", "S", "P", "T", "H", "Y")
)
extractCTDDClass(x, aagroup1 = group1, aagroup2 = group2, aagroup3 = group3)
Run the code above in your browser using DataLab