nhmmer: Calculate likelihood of the given profile hidden markov model...

In MethTargetedNGS: Perform Methylation Analysis on Next Generation Sequencing Data

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 [e-mail]

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}

Example output

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, sd, var, xtabs

The following objects are masked from ‘package:base’:

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:gplots’:

    space

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:seqinr’:

    translate

The following object is masked from ‘package:base’:

    strsplit

MethTargetedNGS documentation built on Nov. 8, 2020, 8:10 p.m.