sigaR: Statistics for Integrative Genomics Analyses in R

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

Author
Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Date of publication
None
Maintainer
Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
License
GPL (>= 2)
Version
1.22.0
URLs

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