# Statistics for Integrative Genomics Analyses in R

## Documentation for package ‘sigaR’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

sigaR-package | statistics for integrative genomics analyses in R
.RCMloss-method | Internal function
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 gene expression.
cisEffectTune | Pre-test and tuning.
cisTest-class | Class "cisTest" for storing the results of the function cisEffectTest.
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 entropyTest.
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.
mutInfTest | Test for mutual information
nBreakpoints | Number of breakpoints
pathway1sample | Penalized estimation of a pathyway's regulatory network from DNA copy number and gene expression data (one-sample).
pathway2sample | Penalized estimation of a pathyway's regulatory network from DNA copy number and gene expression data (two-sample).
pathwayFit-class | Class "pathwayFit" for storing the results of the function pathway1sample or pathway2sample.
pathwayPlot | Plot of the pathyway topology as reconstructed from from DNA copy number and gene expression data (one-sample only).
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 RCMestimation.
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 RCMtest.
sigaR | statistics for integrative genomics analyses in R
splitMatchingAtBreakpoints | Split matching at breakpoints
summary-method | Methods for Function summary
uniqGenomicInfo | Unique genomic location information