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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("sigaR")
AuthorWessel N. van Wieringen <w.vanwieringen@vumc.nl>
Bioconductor views DifferentialExpression GeneExpression Microarray Pathways aCGH
Date of publicationNone
MaintainerWessel N. van Wieringen <w.vanwieringen@vumc.nl>
LicenseGPL (>= 2)
Version1.24.0
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

Functions

cghCall2cghSeg Man page
cghCall2maximumSubset Man page
cghCall2order Man page
cghCall2subset Man page
cghCall2weightedSubset Man page
cghSeg2order Man page
cghSeg2subset Man page
cghSeg2weightedSubset Man page
cisEffectPlot Man page
cisEffectTable Man page
cisEffectTest Man page
cisEffectTune Man page
cisTest-class Man page
CNGEheatmaps Man page
entropyTest Man page
entTest-class Man page
expandMatching2singleIDs Man page
ExpressionSet2order Man page
ExpressionSet2subset Man page
ExpressionSet2weightedSubset Man page
getSegFeatures Man page
hdEntropy Man page
hdMI Man page
matchAnn2Ann Man page
matchCGHcall2ExpressionSet Man page
merge2cghCalls Man page
merge2ExpressionSets Man page
miTest-class Man page
mutInfTest Man page
nBreakpoints Man page
pathway1sample Man page
pathway2sample Man page
pathwayFit-class Man page
pathwayPlot Man page
pollackCN16 Man page
pollackGE16 Man page
profilesPlot Man page
RCMestimation Man page
rcmFit-class Man page
.RCMloss-method Man page
RCMrandom Man page
RCMrandom-method Man page
RCMrandom,rcmFit-method Man page
RCMtest Man page
rcmTest-class Man page
sigaR Man page
sigaR-package Man page
splitMatchingAtBreakpoints Man page
summary,ANY-method Man page
summary,entTest-method Man page
summary-method Man page
summary,miTest-method Man page
summary,rcmFit-method Man page
summary,rcmTest-method Man page
uniqGenomicInfo Man page

Files

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