sigaR: Statistics for Integrative Genomics Analyses in R

Facilitates the joint analysis of high-throughput data from multiple molecular levels. Contains functions for manipulation of objects, various analysis types, and some visualization.

AuthorWessel N. van Wieringen <w.vanwieringen@vumc.nl>
Date of publicationNone
MaintainerWessel N. van Wieringen <w.vanwieringen@vumc.nl>
LicenseGPL (>= 2)
Version1.22.0
http://www.few.vu.nl/~wvanwie

View on Bioconductor

Man pages

cghCall2cghSeg: Genomic ordering of cghSeg-objects.

cghCall2maximumSubset: Maximum subsetting cghCall-objects.

cghCall2order: Genomic ordering of cghCall-objects.

cghCall2subset: Subsetting cghCall-objects.

cghCall2weightedSubset: Weighted subsetting cghCall-objects.

cghSeg2order: Genomic ordering of cghSeg-objects.

cghSeg2subset: Subsetting cghSeg-objects.

cghSeg2weightedSubset: Weighted subsetting cghSeg-objects.

cisEffectPlot: DNA-mRNA plot

cisEffectTable: Table of cis-effect test results

cisEffectTest: Nonparametric testing for copy number induced differential...

cisEffectTune: Pre-test and tuning.

cisTest-class: Class "cisTest" for storing the results of the function...

CNGEheatmaps: Parellel CN and GE heatmap plotting

entropyTest: One-sided two-sample test for entropy comparison

entTest-class: Class "entTest" for storing the results of the function...

expandMatching2singleIDs: Expand matching to single entries

ExpressionSet2order: Genomic ordering of ExpressionSet-objects.

ExpressionSet2subset: Subsetting ExpressionSet-objects.

ExpressionSet2weightedSubset: Weighted subsetting ExpressionSet-objects.

getSegFeatures: Identical signature features selection from cghCall-object.

hdEntropy: Entropy estimation.

hdMI: Mutual information estimation.

matchAnn2Ann: Genomic location matching of two sets of features

matchCGHcall2ExpressionSet: Genomic location matching of CN and GE data

merge2cghCalls: Merge two cghCall-objects into one cghCall-object

merge2ExpressionSets: Merge two ExpressionSet-objects into one ExpressionSet-object

miTest-class: Class "miTest" for storing the results of the function...

mutInfTest: Test for mutual information

nBreakpoints: Number of breakpoints

pathway1sample: Penalized estimation of a pathyway's regulatory network from...

pathway2sample: Penalized estimation of a pathyway's regulatory network from...

pathwayFit-class: Class "pathwayFit" for storing the results of the function...

pathwayPlot: Plot of the pathyway topology as reconstructed from from DNA...

pollackCN16: Breast cancer data (copy number)

pollackGE16: Breast cancer data (gene expression)

profilesPlot: CN-GE profiles plot

RCMestimation: Fitting of the random coefficients model.

rcmFit-class: Class "rcmFit" for storing the results of the function...

RCMrandom: Random data from the random coefficients model.

RCMrandom-method: Methods for Function RCMrandom

RCMtest: Hypothesis testing within the random coefficient model.

rcmTest-class: Class "rcmTest" for storing the results of the function...

sigaR-package: statistics for integrative genomics analyses in R

splitMatchingAtBreakpoints: Split matching at breakpoints

summary-method: Methods for Function summary

uniqGenomicInfo: Unique genomic location information

z.RCMloss-method: Internal function

Files in this package

sigaR/DESCRIPTION
sigaR/NAMESPACE
sigaR/R
sigaR/R/cisEffectFunctions.R
sigaR/R/classDefinitions.r
sigaR/R/dataManagementFunctions.r
sigaR/R/entropyFunctions.r
sigaR/R/pathwayFunctions.R
sigaR/R/plotFunctions.r
sigaR/R/private.R sigaR/R/privateCisEffectFunctions.R
sigaR/R/rcmFunctions.r
sigaR/build
sigaR/build/vignette.rds
sigaR/data
sigaR/data/pollackCN16.rda
sigaR/data/pollackGE16.rda
sigaR/inst
sigaR/inst/CITATION
sigaR/inst/doc
sigaR/inst/doc/sigaR.R
sigaR/inst/doc/sigaR.Rnw
sigaR/inst/doc/sigaR.pdf
sigaR/man
sigaR/man/CNGEheatmaps.Rd sigaR/man/ExpressionSet2order.Rd sigaR/man/ExpressionSet2subset.Rd sigaR/man/ExpressionSet2weightedSubset.Rd sigaR/man/RCMestimation.Rd sigaR/man/RCMrandom-method.Rd sigaR/man/RCMrandom.Rd sigaR/man/RCMtest.Rd sigaR/man/cghCall2cghSeg.Rd sigaR/man/cghCall2maximumSubset.Rd sigaR/man/cghCall2order.Rd sigaR/man/cghCall2subset.Rd sigaR/man/cghCall2weightedSubset.Rd sigaR/man/cghSeg2order.Rd sigaR/man/cghSeg2subset.Rd sigaR/man/cghSeg2weightedSubset.Rd sigaR/man/cisEffectPlot.Rd sigaR/man/cisEffectTable.Rd sigaR/man/cisEffectTest.Rd sigaR/man/cisEffectTune.Rd sigaR/man/cisTest-class.Rd sigaR/man/entTest-class.Rd sigaR/man/entropyTest.Rd sigaR/man/expandMatching2singleIDs.Rd sigaR/man/getSegFeatures.Rd sigaR/man/hdEntropy.Rd sigaR/man/hdMI.Rd sigaR/man/matchAnn2Ann.Rd sigaR/man/matchCGHcall2ExpressionSet.Rd sigaR/man/merge2ExpressionSets.Rd sigaR/man/merge2cghCalls.Rd sigaR/man/miTest-class.Rd sigaR/man/mutInfTest.Rd sigaR/man/nBreakpoints.Rd sigaR/man/pathway1sample.Rd sigaR/man/pathway2sample.Rd sigaR/man/pathwayFit-class.Rd sigaR/man/pathwayPlot.Rd sigaR/man/pollackCN16.Rd sigaR/man/pollackGE16.Rd sigaR/man/profilesPlot.Rd sigaR/man/rcmFit-class.Rd sigaR/man/rcmTest-class.Rd sigaR/man/sigaR-package.Rd sigaR/man/splitMatchingAtBreakpoints.Rd sigaR/man/summary-method.Rd sigaR/man/uniqGenomicInfo.Rd sigaR/man/z.RCMloss-method.Rd
sigaR/vignettes
sigaR/vignettes/sigaR.Rnw
sigaR/vignettes/statisticalUnit.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.