OrderedList: Similarities of Ordered Gene Lists

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.

Author
Xinan Yang, Stefanie Scheid, Claudio Lottaz
Date of publication
None
Maintainer
Claudio Lottaz <Claudio.Lottaz@klinik.uni-regensburg.de>
License
GPL (>= 2)
Version
1.46.0
URLs

View on Bioconductor

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

Files in this package

OrderedList/DESCRIPTION
OrderedList/NAMESPACE
OrderedList/R
OrderedList/R/OrderedList.R
OrderedList/R/a.R
OrderedList/R/compareLists.R
OrderedList/R/getOverlap.R
OrderedList/R/plot.OrderedList.R
OrderedList/R/prepareData.R
OrderedList/R/print.OrderedList.R
OrderedList/build
OrderedList/build/vignette.rds
OrderedList/data
OrderedList/data/OL.data.rda
OrderedList/data/OL.result.rda
OrderedList/inst
OrderedList/inst/R-script
OrderedList/inst/R-script/makedata.R
OrderedList/inst/doc
OrderedList/inst/doc/tr_2006_01.R
OrderedList/inst/doc/tr_2006_01.Rnw
OrderedList/inst/doc/tr_2006_01.pdf
OrderedList/man
OrderedList/man/OL.data.Rd
OrderedList/man/OL.result.Rd
OrderedList/man/OrderedList.Rd
OrderedList/man/check.test.args.Rd
OrderedList/man/compareLists.Rd
OrderedList/man/getOverlap.Rd
OrderedList/man/overlap.Rd
OrderedList/man/plot.OrderedList.Rd
OrderedList/man/prepareData.Rd
OrderedList/man/preparePermutations.Rd
OrderedList/man/print.OrderedList.Rd
OrderedList/man/scoreOrderComparison.Rd
OrderedList/man/scoreRankings.Rd
OrderedList/man/shuffledRandomScores.Rd
OrderedList/vignettes
OrderedList/vignettes/MPIMG_logo.png
OrderedList/vignettes/Makefile
OrderedList/vignettes/bcb_logo.pdf
OrderedList/vignettes/compdiag.sty
OrderedList/vignettes/tr_2006_01.Rnw