krm (version 2022.10-17)

getSeqKernel: Protein Sequence Kernels

Description

Get mutual information and other kernels for protein sequences

Usage

getSeqKernel (sequences, kern.type=c("mm", "prop", "mi"), tau, call.C=TRUE
    , seq.start=NULL, seq.end=NULL)

Arguments

sequences

String or list. If string, the name of a fasta file containing aligned sequences. If list, a list of strings, each string is a protein sequence. If list, call.C will be set to FALSE internally because C/C++ function needs sequence file name as input

kern.type

string. Type of kernel. mm: match-mismatch, prop: physicochemical properties, mi: mutual information.

tau

Numeric. It is the same as rho^-2.

call.C

Boolean. If TRUE, do a .C call. If FALSE, the implementation is in R. The .C call is 50 times faster.

seq.start

integer. Start position of subsequence to be used in computing kernel.

seq.end

integer. End position of subsequence to be used in computing kernel.

Details

call.C option is to allow comparison of R and C implementation. The two should give the same results and C implementation is 50 times faster.

when kern.type is mi and call.C is TRUE and when running on linux, this function will print messages like "read ...". This message is generated from U::openRead

Examples

fileName=paste(system.file(package="krm")[1],'/misc/SETpfamseed_aligned_for_testing.fasta',
     sep="")
K=getSeqKernel (fileName, kern.type="mi", tau=1, call.C=TRUE)
K