featureGapPairComposition {BioSeqClass} | R Documentation |
Sequences are coded based on the frequency of g-spaced aminoacids/bases pairs.
featureGapPairComposition(seq,g,class=elements("aminoacid"))
seq |
a string vector for the protein, DNA, or RNA sequences. |
g |
an integer indicating the distance between two aminoacids/bases (g>=0). |
class |
a list for the class of biological properties. It can
be produced by |
featureGapPairComposition
returns a matrix with M\^2 columns.
Each row represented features of one sequence coding by a M\^2 dimension
numeric vector. Each column is the frequency of g-spaced aminoacids/bases
pair. featureFragmentComposition(seq,2) is same with featureGapPairComposition(seq,0).
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] GPC0 = featureGapPairComposition(seq,0,elements("aminoacid")) GPC2 = featureGapPairComposition(seq,2,elements("aminoacid")) }