motifcounter

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see motifcounter.

R package for analysing TFBSs in DNA sequences


Bioconductor version: 3.7

'motifcounter' provides functionality to compute the statistics related with motif matching and counting of motif matches in DNA sequences. As an input, 'motifcounter' requires a motif in terms of a position frequency matrix (PFM). Furthermore, a set of DNA sequences is required to estimated a higher-order background model (BGM). The package provides functions to investigate the the per-position and per strand log-likelihood scores between the PFM and the BGM across a given sequence of set of sequences. Furthermore, the package facilitates motif matching based on an automatically derived score threshold. To this end the distribution of scores is efficiently determined and the score threshold is chosen for a user-prescribed significance level. This allows to control for the false positive rate. Moreover, 'motifcounter' implements a motif match enrichment test based on two the number of motif matches that are expected in random DNA sequences. Motif enrichment is facilitated by either a compound Poisson approximation or a combinatorial approximation of the motif match counts. Both models take higher-order background models, the motif's self-similarity, and hits on both DNA strands into account. The package is in particular useful for long motifs and/or relaxed choices of score thresholds, because the implemented algorithms efficiently bypass the need for enumerating a (potentially huge) set of DNA words that can give rise to a motif match.

Author: Wolfgang Kopp [aut, cre]

Maintainer: Wolfgang Kopp <wolfgang.kopp at mdc-berlin.de>

Citation (from within R, enter citation("motifcounter")):

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("motifcounter")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("motifcounter")
Introduction to the `motifcounter` package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews MotifAnnotation, SequenceMatching, Software, Transcription
Version 1.4.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-2
Depends R (>= 3.0)
Imports Biostrings, methods
System Requirements
URL
See More
Suggests knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package motifcounter_1.4.0.tar.gz
Windows Binary motifcounter_1.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) motifcounter_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/motifcounter
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/motifcounter
Package Short Url https://bioconductor.org/packages/motifcounter/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive