pcaGoPromoter: pcaGoPromoter is used to analyze DNA micro array data
Version 1.20.0

This package contains functions to ease the analyses of DNA micro arrays. It utilizes principal component analysis as the initial multivariate analysis, followed by functional interpretation of the principal component dimensions with overrepresentation analysis for GO terms and regulatory interpretations using overrepresentation analysis of predicted transcription factor binding sites with the primo algorithm.

AuthorMorten Hansen, Jorgen Olsen
Bioconductor views GO GeneExpression Microarray Visualization
Date of publicationNone
MaintainerMorten Hansen <mhansen@sund.ku.dk>
LicenseGPL (>= 2)
Version1.20.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("pcaGoPromoter")

Getting started

Package overview

Popular man pages

GOtree: GOtree, plot.GOtree and GOtreeWithLeaveOneOut
pca: pca - Principal Component Analysis (PCA)
pcaGoPromoter-package: Tools for analyzing data from DNA micro arrays.
primo: primo, primoHits and primoWithLeaveOut
primoData: primoData
See all...

All man pages Function index File listing

Man pages

GOtree: GOtree, plot.GOtree and GOtreeWithLeaveOneOut
pca: pca - Principal Component Analysis (PCA)
pcaGoPromoter-package: Tools for analyzing data from DNA micro arrays.
primo: primo, primoHits and primoWithLeaveOut
primoData: primoData

Functions

GOtree Man page Source code
GOtreeHits Man page Source code
GOtreeWithLeaveOut Man page Source code
cleanUpTargetSet Source code
convertFromProbeIdsToRefseqs Source code
convertInput Source code
dropVarNull Source code
getGOidsInOntology Source code
getGOidsWithChildren Source code
getGOsDownTree Source code
getMatricesWithHits Source code
getRankedProbeIds Man page Source code
getRankedProbeIds.pca Man page Source code
getSigGOTermsOnce Source code
indexOfDupletsList Source code
leaveOutFindPvalues Source code
makeGOtreeRgraphviz Source code
multiPca Source code
newSearchGOtreeForTerms Source code
pca Man page Source code
pcaGoPromoter Man page
pcaGoPromoter-package Man page
pcaInfoPlot Man page Source code
pcaLeaveOut Source code
plot.GOtree Man page Source code
plot.pca Man page Source code
primo Man page Source code
primoData Man page Source code
primoData.convertPromoterFromTextToNumbers Source code
primoData.convertToNumbers Source code
primoData.findDubletSequences Source code
primoData.findDublets Source code
primoData.getAllThresholds Source code
primoData.getPromoters Source code
primoData.getPwmValuesInPromotersFast Source code
primoData.getThresholdNew Source code
primoData.removeBadSequences Source code
primoHits Man page Source code
primoWithLeaveOut Man page Source code
print.GOtree Man page Source code
print.pca Man page Source code
printAnnText Source code
printAnnotation Source code

Files

DESCRIPTION
NAMESPACE
R
R/GOtree.R
R/common.R
R/pca.R
R/primo.R
R/primoData.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/pcaGoPromoter.R
inst/doc/pcaGoPromoter.Rnw
inst/doc/pcaGoPromoter.pdf
man
man/GOtree.Rd
man/pca.Rd
man/pcaGoPromoter-package.Rd
man/primo.Rd
man/primoData.Rd
vignettes
vignettes/pcaGoPromoter.Rnw
pcaGoPromoter documentation built on May 20, 2017, 9:15 p.m.

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