Man pages for BIMSBbioinfo/reg2gene
Predicting the target genes for regulatory elements
| annotateInteractionsToGenes | Annotate interaction set to genes reported in geneAnnotation |
| annotateToPromoter | Annotate genomic location(windows) to genes reported in... |
| associateReg2Gene | Associate regulatory regions to genes |
| assocTable2 | this function creates a table of keys and pvals from a... |
| benchmarkInteractions | Benchmarks interactions reg2gene models using benchmark data |
| benchmarkInteractionssimple | Benchmarks help function |
| benchPlotHelp | Plots enhancer-promoter interactions |
| bwToGeneExp | Quantifies gene expression measured by RNA-Seq |
| compareModelStat | Reports a number of statistically significant enhancer~... |
| compareReg2Traits | Compare two objects of genomic region~gene~trait associations |
| confusionMatrix | ConfusionTable statistics for the benchmarked interactions... |
| corMat | Correlation between a col matrix and a vector |
| corResample | Correlation with resampling p-values |
| createIntTrack | Help function to create InteractionTrack |
| dcorMat | Distance correlation between a col matrix and a vector |
| dcorResample | Distance correlation with resampling based p-values |
| detectGeneEnhPresence | GRanges contains gene+enhancer info |
| estimateGammaPval | Estimate P-values from resampling statistics using Gamma... |
| exonExpressionStrandAdjusted | Function that quantifies exon expression based on strand... |
| extractInfo | Help f() to extract info about cohort/method/algorithm |
| filterPreBenchGIsimple | Filtering help function |
| forceByname | Benchmarks help function - forceByName |
| getGeneEnhScoresDF | extract gene-enhancer scores from GRanges object |
| getStatistics | Selects column that will be used as an input to plot heigth... |
| gettingGeneInfoEnsembl | Help function to get info about exon location for genes of... |
| getTSS | My stupid help function to get TSS for lists of enhancer~gene... |
| glmnetResample | internal function that uses glmnet for prediction |
| grlist2GI | convert GRangesList to GInteractions |
| grlist2gr | convert GRangesList to GRanges with associated regulatory... |
| GRReg1_toy | GRanges example to test various functions from reg2gene |
| GRReg2_toy | Sample file for benchmark dataset |
| grReorg | Help for grlist2gr() |
| makeIndexTable | Creates Index table of files produced by reg2gene data... |
| manyZeros | decide if the input colum from a matrix has many zeros |
| metaInteractions | meta-analysis for regulatory region and gene interactions |
| ModellingTest | GRanges example to test modelling of associateReg2gene... |
| normalizeScores | Function that runs normalization for the quantified... |
| perGeneModelling | Function returns output of called modelling procedure... |
| plotGEEA | Scatterplots of enhancer activity~gene expression for max 16... |
| plotInteractions | Plots enhancer-promoter interactions |
| quantifyGeneExpression | Function that quantifies gene expression based on... |
| qvaluCal | internal qvalue calculation function |
| reg2gene | Hierarchically annotates input GRanges object with... |
| reg2trait | Add associated traits to the interaction object |
| regActivity | Calculates regulatory activity over pre-defined regions |
| regActivityAroundTSS | Identify regulatory regions around provided TSSes |
| rfResample | internal RandomForest prediction function |
| scoresAsMcols | Function that rearranges list of scores calculated per cell... |
| selectEP | Returns N TOP/BOTTOM/RANDOM associations per... |
| selectGeneF | Selects genes of interest and associated reg regions from... |
| selectRegR | Selects reg regions of interest from GInteractions obj,and... |
| setColors | Adjusts for colors of plot: three options: 1) all red, in not... |
| stepwise.complete.cases | Stepwise complete cases method |
| votedEP | Returns voted EP pairs for the combination of cohort/method/... |
| voteInteractions | Majority vote decision for (regulatory region)-gene... |
| zeroVar | decide if the input colum matrix has zero variation |
