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

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}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(MethTargetedNGS)
Loading required package: stringr
Loading required package: seqinr
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:gplots':

    space

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:seqinr':

    translate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MethTargetedNGS/nhmmer.Rd_%03d_medium.png", width=480, height=480)
> ### Name: nhmmer
> ### Title: Calculate likelihood of the given profile hidden markov model
> ###   against group of sequences
> ### Aliases: nhmmer
> ### Keywords: HMMER ProfileHMM Methylation
> 
> ### ** 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}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>