OrderedList: Similarities of Ordered Gene Lists
Version 1.48.0

Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.

Browse man pages Browse package API and functions Browse package files

AuthorXinan Yang, Stefanie Scheid, Claudio Lottaz
Bioconductor views DifferentialExpression Microarray MultipleComparison
Date of publicationNone
MaintainerClaudio Lottaz <Claudio.Lottaz@klinik.uni-regensburg.de>
LicenseGPL (>= 2)
Version1.48.0
URL http://compdiag.molgen.mpg.de/software/index.shtml
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("OrderedList")

Man pages

check.test.args: Helper Function to Compute Test Statistics
compareLists: Compare Ordered Lists with Weighted Overlap Score
getOverlap: Extracting the Intersecting IDs From a listComparison Object
OL.data: Gene Expression and Clinical Information of Two Cancer...
OL.result: Three Examples of Class 'OrderedList'
OrderedList: Detecting Similarities of Two Microarray Studies
overlap: Count Elements in Overlap between two Lists
plot.OrderedList: Plotting Function for OrderedList Objects
prepareData: Combining Two Studies into an Expression Set
preparePermutations: Prepare Permutation and Subsetting Matrices
print.OrderedList: Printing Function for OrderedList Objects
scoreOrderComparison: Score the Comparison of two Gene Rankings
scoreRankings: Score the Comparison of two Rankings
shuffledRandomScores: Generates Null-Distribution for List-Overlap-Scores

Functions

First.lib Source code
OL.data Man page
OL.result Man page
OrderedList Man page Source code
check.test.args Man page Source code
compareLists Man page Source code
getOverlap Man page Source code
overlap Man page Source code
plot.OrderedList Man page Source code
plot.listComparison Man page Source code
plot.listComparisonOverlap Man page Source code
plot.shuffledRandomScores Man page Source code
prepareData Man page Source code
preparePermutations Man page Source code
print.OrderedList Man page Source code
print.listComparison Man page Source code
print.listComparisonOverlap Man page Source code
print.shuffledRandomScores Man page Source code
scoreOrderComparison Man page Source code
scoreOrderComparisonBoth Man page Source code
scoreRankings Man page Source code
shuffledRandomScores Man page Source code
test.fc Man page Source code
test.t Man page Source code
test.z Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/OrderedList.R
R/a.R
R/compareLists.R
R/getOverlap.R
R/plot.OrderedList.R
R/prepareData.R
R/print.OrderedList.R
build
build/vignette.rds
data
data/OL.data.rda
data/OL.result.rda
inst
inst/R-script
inst/R-script/makedata.R
inst/doc
inst/doc/tr_2006_01.R
inst/doc/tr_2006_01.Rnw
inst/doc/tr_2006_01.pdf
man
man/OL.data.Rd
man/OL.result.Rd
man/OrderedList.Rd
man/check.test.args.Rd
man/compareLists.Rd
man/getOverlap.Rd
man/overlap.Rd
man/plot.OrderedList.Rd
man/prepareData.Rd
man/preparePermutations.Rd
man/print.OrderedList.Rd
man/scoreOrderComparison.Rd
man/scoreRankings.Rd
man/shuffledRandomScores.Rd
vignettes
vignettes/MPIMG_logo.png
vignettes/Makefile
vignettes/bcb_logo.pdf
vignettes/compdiag.sty
vignettes/tr_2006_01.Rnw
OrderedList documentation built on May 20, 2017, 10:59 p.m.