profileScoreDist: Profile score distributions
Version 1.4.0

Regularization and score distributions for position count matrices.

AuthorPaal O. Westermark
Bioconductor views GeneRegulation Software StatisticalMethod
Date of publicationNone
MaintainerPaal O. Westermark <pal-olof.westermark@charite.de>
LicenseMIT + file LICENSE
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("profileScoreDist")

Getting started

Using profileScoreDist

Popular man pages

backgroundDist: Background distribution.
INR: The position count matrix for INR.
plotDist: Plot background and signal distributions.
ProfileDist-class: ProfileDist
regularizeMatrix: Careful regularization (pseudocount addition) to a position...
scoreDistCutoffs: False discovery rate and power for PWM Score distributions.
signalDist: Signal distribution.
See all...

All man pages Function index File listing

Man pages

backgroundDist: Background distribution.
computeScoreDist: Compute exact position weight/count matrix score...
INR: The position count matrix for INR.
plotDist: Plot background and signal distributions.
ProfileDist-class: ProfileDist
regularizeMatrix: Careful regularization (pseudocount addition) to a position...
scoreDistCutoffs: False discovery rate and power for PWM Score distributions.
signalDist: Signal distribution.

Functions

INR Man page
ProfileDist Man page
ProfileDist-class Man page
backgroundDist Man page
backgroundDist,ProfileDist-method Man page
computeDelta Source code
computeDeltadiff Source code
computeScoreDist Man page Source code
computew Source code
plotDist Man page
plotDist,ProfileDist-method Man page
profileConvolution Source code
profilePosscoreprob Source code
pwmFormatCheck Source code
regularizeMatrix Man page Source code
regularizeRow Source code
score,ProfileDist-method Man page
scoreDistCutoffs Man page Source code
show,ProfileDist-method Man page
signalDist Man page
signalDist,ProfileDist-method Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/RcppExports.R
R/data.R
R/profileDist-class.R
R/profileScoreDist.R
build
build/vignette.rds
data
data/INR.rda
inst
inst/NEWS
inst/doc
inst/doc/profileScoreDist-vignette.R
inst/doc/profileScoreDist-vignette.Rmd
inst/doc/profileScoreDist-vignette.pdf
man
man/INR.Rd
man/ProfileDist-class.Rd
man/backgroundDist.Rd
man/computeScoreDist.Rd
man/plotDist.Rd
man/regularizeMatrix.Rd
man/scoreDistCutoffs.Rd
man/signalDist.Rd
src
src/RcppExports.cpp
src/profileConvolution.cpp
src/profilePosscoreprob.cpp
vignettes
vignettes/profileScoreDist-vignette.Rmd
profileScoreDist documentation built on May 20, 2017, 10:14 p.m.

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