Man pages for sigaR
Statistics for Integrative Genomics Analyses in R
| 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 |
