getSeqKernel: Protein Sequence Kernels

In krm: Kernel Based Regression Models

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

krm documentation built on Oct. 18, 2022, 9:09 a.m.