featureFragmentComposition {BioSeqClass} | R Documentation |
Sequences are coded based on the frequency of k-mer sequence fragments.
featureFragmentComposition(seq,k,class=elements("aminoacid"))
seq |
a string vector for the protein, DNA, or RNA sequences. |
k |
an integer indicating the length of sequence fragment (k>=1). |
class |
a list for the class of biological properties. It can
be produced by |
featureFragmentComposition
returns a matrix with M\^k columns.
Each row represented features of one sequence coding by a M\^k dimension
numeric vector. Each column is the frequency of k-mer sequence fragment.
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] FC2 = featureFragmentComposition(seq,2,aaClass("aaS")) FC3 = featureFragmentComposition(seq,3,aaClass("aaS")) }