featurePseudoAAComp {BioSeqClass} | R Documentation |
Protein sequences are coded by pseudo amino acid composiion.
featurePseudoAAComp(seq,d,w=0.05)
seq |
a string vector for the protein, DNA, or RNA sequences. |
d |
an integer used as paramter of |
w |
a numeric value for the weight factor of sequence order effect in
|
featurePseudoAAComp
returns a matrix representing the pseudo
amino acid composiion. Each row represented features of one sequence coding
by a 20+d dimension numeric vector. The first 20 features indicates the
composition of 20 amino acids. The last d features indicates the coupling
between amino acids X(i) and X(i+d). Coupling value is cacluated by hydrophobicity,
hydrophilicity and mass of amino acids.
Hong Li
if(interactive()){ file = file.path(path.package("BioSeqClass"), "example", "acetylation_K.pos40.pep") seq = as.matrix(read.csv(file,header=F,sep="\t",row.names=1))[,1] PAC4 = featurePseudoAAComp(seq,4) }