nhmmer {MethTargetedNGS}R Documentation

Calculate likelihood of the given profile hidden markov model against group of sequences

Description

This function calculates likelihood score of given pool of sequences against given profile hidden markov model using HMMER algorithm.[1]

Usage

nhmmer(file_hmm, file_seq, pathHMMER="")

Arguments

file_hmm

HMM file from hmmbuild function

file_seq

Sequence fasta file for calculating likelihood

pathHMMER

Path where HMMER software is installed. Note: Windows user must setup cygwin to use this feature and set path to HMMER binaries ( ~hmmer/binaries/)

Value

Matrix containing likelihood scores

Note

Require HMMER software

Windows User: Please download HMMER from http://hmmer.janelia.org/

Setup cygwin from http://www.cygwin.com

Linux/Mac User: Download binaries or compile HMMER from http://hmmer.janelia.org/

Author(s)

Muhammad Ahmer Jamil, Prof. Holger Frohlich, Priv.-Doz. Dr. Osman El-Maarri

Maintainer: Muhammad Ahmer Jamil engr.ahmerjamil@gmail.com

References

[1]Finn, Robert D., Jody Clements, and Sean R. Eddy. "HMMER web server: interactive sequence similarity searching." Nucleic acids research (2011): gkr367.

See Also

hmmbuild

Examples

msa = system.file("extdata", "msa.fasta", package = "MethTargetedNGS")
tumor = system.file("extdata", "Tumor.fasta", package = "MethTargetedNGS")
if (file.exists("/usr/bin/hmmbuild"))
{hmmbuild(file_seq=msa,file_out="hmm",pathHMMER = "/usr/bin")
res <- nhmmer("hmm",tumor,pathHMMER = "/usr/bin")
res}

[Package MethTargetedNGS version 1.16.0 Index]