featureHydro {BioSeqClass} | R Documentation |
Protein sequences are coded based on their hydrophobicity.
featureHydro(seq,hydro.method="SARAH1") featureACH(seq,hydro.index="hydroE")
seq |
a string vector for the protein, DNA, or RNA sequences. |
hydro.method |
a string for the method of coding protein hydrophobic effect. This must be one of the strings "kpm" or "SARAH1". |
hydro.index |
a string for the method of coding protein hydrophobic effect. This must be one of the strings "hydroE", "hydroF" or "hydroC". |
featureHydro
returns a matrix measuring the hydrophobic effect.
Parameter "hydro.method" supported following coding methods:
"kpm": use a numeral to indicating the hydrophobic effect of amino acid. Each
sequence is coded by a N dimension numeric vector.
"SARAH1": use a 5 dimension 0-1 vector to indicating the hydrophobic effect of
amino acid. Each sequence is coded by a 5*N dimension 0-1 vector.
featureACH
returns a matrix with (N-1)/2 columns. N is the
length of input sequence, andis N must be odd. Central residue of all
windows are the central residue of input sequence. Each column is
the average cumulative hydrophobicity over a sliding window.
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] H1 = featureHydro(seq,"kpm") H2 = featureHydro(seq,"SARAH1") H3 = featureACH(seq,hydro.index="hydroE") H3 = featureACH(seq,hydro.index="hydroF") H3 = featureACH(seq,hydro.index="hydroC") }