Package: motifcounter
Type: Package
Title: R package for analysing TFBSs in DNA sequences
Version: 1.0.0
Date: 2016
Author: Wolfgang Kopp [aut, cre]
Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
Imports: Biostrings, methods
Depends: R(>= 3.0)
Maintainer: Wolfgang Kopp <kopp@molgen.mpg.de>
Description: '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.
License: GPL-2
biocViews: Transcription,MotifAnnotation,SequenceMatching,Software
RoxygenNote: 5.0.1
VignetteBuilder: knitr
NeedsCompilation: yes
Collate: 'background_wrapper.R' 'comppoiss_wrapper.R'
        'combinatorial_wrapper.R' 'score_wrapper.R' 'count_wrapper.R'
        'enrichmentTest.R' 'forground_wrapper.R'
        'motifcounter-package.R' 'observed_wrapper.R' 'option.R'
        'overlap.R' 'simulate_wrapper.R' 'wrapper.R'
Packaged: 2017-04-25 01:53:03 UTC; biocbuild
Built: R 3.4.0; i386-w64-mingw32; 2017-04-25 05:41:24 UTC; windows
Archs: i386, x64
