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sigaR (version 1.18.0)

Statistics for Integrative Genomics Analyses in R

Description

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

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Version

Version

1.18.0

License

GPL (>= 2)

Maintainer

Wessel van Wieringen

Last Published

February 15th, 2017

Functions in sigaR (1.18.0)

matchAnn2Ann

Genomic location matching of two sets of features
cghCall2maximumSubset

Maximum subsetting cghCall-objects.
RCMtest

Hypothesis testing within the random coefficient model.
RCMestimation

Fitting of the random coefficients model.
cghCall2subset

Subsetting cghCall-objects.
ExpressionSet2weightedSubset

Weighted subsetting ExpressionSet-objects.
getSegFeatures

Identical signature features selection from cghCall-object.
expandMatching2singleIDs

Expand matching to single entries
pollackCN16

Breast cancer data (copy number)
cghSeg2subset

Subsetting cghSeg-objects.
CNGEheatmaps

Parellel CN and GE heatmap plotting
cisEffectPlot

DNA-mRNA plot
ExpressionSet2subset

Subsetting ExpressionSet-objects.
splitMatchingAtBreakpoints

Split matching at breakpoints
cisTest-class

Class "cisTest" for storing the results of the function cisEffectTest.
cghCall2order

Genomic ordering of cghCall-objects.
pathwayFit-class

Class "pathwayFit" for storing the results of the function pathway1sample or pathway2sample.
cisEffectTable

Table of cis-effect test results
cisEffectTest

Nonparametric testing for copy number induced differential gene expression.
pathway1sample

Penalized estimation of a pathyway's regulatory network from DNA copy number and gene expression data (one-sample).
hdMI

Mutual information estimation.
sigaR-package

statistics for integrative genomics analyses in R
cghCall2cghSeg

Genomic ordering of cghSeg-objects.
nBreakpoints

Number of breakpoints
uniqGenomicInfo

Unique genomic location information
rcmFit-class

Class "rcmFit" for storing the results of the function RCMestimation.
cisEffectTune

Pre-test and tuning.
cghSeg2weightedSubset

Weighted subsetting cghSeg-objects.
cghCall2weightedSubset

Weighted subsetting cghCall-objects.
.RCMloss-method

Internal function
pathway2sample

Penalized estimation of a pathyway's regulatory network from DNA copy number and gene expression data (two-sample).
profilesPlot

CN-GE profiles plot
cghSeg2order

Genomic ordering of cghSeg-objects.
pathwayPlot

Plot of the pathyway topology as reconstructed from from DNA copy number and gene expression data (one-sample only).
mutInfTest

Test for mutual information
matchCGHcall2ExpressionSet

Genomic location matching of CN and GE data
entropyTest

One-sided two-sample test for entropy comparison
pollackGE16

Breast cancer data (gene expression)
summary-method

Methods for Function summary
RCMrandom-method

Methods for Function RCMrandom
RCMrandom

Random data from the random coefficients model.
entTest-class

Class "entTest" for storing the results of the function entropyTest.
hdEntropy

Entropy estimation.
merge2ExpressionSets

Merge two ExpressionSet-objects into one ExpressionSet-object
miTest-class

Class "miTest" for storing the results of the function mutInfTest.
ExpressionSet2order

Genomic ordering of ExpressionSet-objects.
rcmTest-class

Class "rcmTest" for storing the results of the function RCMtest.
merge2cghCalls

Merge two cghCall-objects into one cghCall-object