statistics for integrative genomics analyses in R


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Documentation for package ‘sigaR’ version 1.0.0

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sigaR-package statistics for integrative genomics analyses in R
.RCMloss-method Internal function
cghCall2maximumSubset Maximum subsetting cghCall-objects.
cghCall2order Genomic ordering of cghCall-objects.
cghCall2subset Subsetting cghCall-objects.
cghCall2weightedSubset Weighted subsetting cghCall-objects.
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
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