Man pages for BIMSBbioinfo/reg2gene
Predicting the target genes for regulatory elements

annotateInteractionsToGenesAnnotate interaction set to genes reported in geneAnnotation
annotateToPromoterAnnotate genomic location(windows) to genes reported in...
associateReg2GeneAssociate regulatory regions to genes
assocTable2this function creates a table of keys and pvals from a...
benchmarkInteractionsBenchmarks interactions reg2gene models using benchmark data
benchmarkInteractionssimpleBenchmarks help function
benchPlotHelpPlots enhancer-promoter interactions
bwToGeneExpQuantifies gene expression measured by RNA-Seq
compareModelStatReports a number of statistically significant enhancer~...
compareReg2TraitsCompare two objects of genomic region~gene~trait associations
confusionMatrixConfusionTable statistics for the benchmarked interactions...
corMatCorrelation between a col matrix and a vector
corResampleCorrelation with resampling p-values
createIntTrackHelp function to create InteractionTrack
dcorMatDistance correlation between a col matrix and a vector
dcorResampleDistance correlation with resampling based p-values
detectGeneEnhPresenceGRanges contains gene+enhancer info
estimateGammaPvalEstimate P-values from resampling statistics using Gamma...
exonExpressionStrandAdjustedFunction that quantifies exon expression based on strand...
extractInfoHelp f() to extract info about cohort/method/algorithm
filterPreBenchGIsimpleFiltering help function
forceBynameBenchmarks help function - forceByName
getGeneEnhScoresDFextract gene-enhancer scores from GRanges object
getStatisticsSelects column that will be used as an input to plot heigth...
gettingGeneInfoEnsemblHelp function to get info about exon location for genes of...
getTSSMy stupid help function to get TSS for lists of enhancer~gene...
glmnetResampleinternal function that uses glmnet for prediction
grlist2GIconvert GRangesList to GInteractions
grlist2grconvert GRangesList to GRanges with associated regulatory...
GRReg1_toyGRanges example to test various functions from reg2gene
GRReg2_toySample file for benchmark dataset
grReorgHelp for grlist2gr()
makeIndexTableCreates Index table of files produced by reg2gene data...
manyZerosdecide if the input colum from a matrix has many zeros
metaInteractionsmeta-analysis for regulatory region and gene interactions
ModellingTestGRanges example to test modelling of associateReg2gene...
normalizeScoresFunction that runs normalization for the quantified...
perGeneModellingFunction returns output of called modelling procedure...
plotGEEAScatterplots of enhancer activity~gene expression for max 16...
plotInteractionsPlots enhancer-promoter interactions
quantifyGeneExpressionFunction that quantifies gene expression based on...
qvaluCalinternal qvalue calculation function
reg2geneHierarchically annotates input GRanges object with...
reg2traitAdd associated traits to the interaction object
regActivityCalculates regulatory activity over pre-defined regions
regActivityAroundTSSIdentify regulatory regions around provided TSSes
rfResampleinternal RandomForest prediction function
scoresAsMcolsFunction that rearranges list of scores calculated per cell...
selectEPReturns N TOP/BOTTOM/RANDOM associations per...
selectGeneFSelects genes of interest and associated reg regions from...
selectRegRSelects reg regions of interest from GInteractions obj,and...
setColorsAdjusts for colors of plot: three options: 1) all red, in not...
stepwise.complete.casesStepwise complete cases method
votedEPReturns voted EP pairs for the combination of cohort/method/...
voteInteractionsMajority vote decision for (regulatory region)-gene...
zeroVardecide if the input colum matrix has zero variation
BIMSBbioinfo/reg2gene documentation built on May 10, 2018, 8:02 a.m.