Binned Motif Enrichment Analysis and Visualization


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Documentation for package ‘monaLisa’ version 1.0.0

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monaLisa-package monaLisa - MOtif aNAlysis with Lisa.
annoSeqlogo Sequence logo annotation
bin Bin elements of 'x'.
calcBinnedKmerEnr Calculate k-mer enrichment in bins of sequences.
calcBinnedMotifEnrHomer Prepare and run HOMER motif enrichment analysis.
calcBinnedMotifEnrR Binned Motif Enrichment Analysis with 'monaLisa'
dumpJaspar Dump Jaspar motifs into a HOMER motif file.
findHomer Find HOMER script file.
findMotifHits Find motif matches in sequences.
findMotifHits-method Find motif matches in sequences.
getColsByBin Get colors by bin.
getKmerFreq Calculate observed and expected k-mer frequencies
getSetZeroBin Get and set the zero bin manually
getZeroBin Get and set the zero bin manually
homerToPFMatrixList Read a HOMER motif file and create a PFMatrixList
monaLisa monaLisa - MOtif aNAlysis with Lisa.
motifKmerSimilarity Calculate similarities between motifs and k-mers.
motifSimilarity Calculate similarities between pairs of motifs.
parseHomerOutput load output from HOMER findMotifsGenome.pl into R
plotBinDensity Density plot of binned elements.
plotBinDiagnostics Plot diagnostics of binned sequences
plotBinHist Histogram of binned elements.
plotBinScatter Scatter plot (xy-plot) of binned elements.
plotMotifHeatmaps Heatmap of motif enrichments.
plotSelectionProb Plot selection probabilities of predictors
plotStabilityPaths Plot Stability Paths
prepareHomer Prepare input files for HOMER motif enrichment analysis.
randLassoStabSel Randomized Lasso Stability Selection
sampleRandomRegions Sample random regions of fixed length.
seqLogoGrob Create a simple sequence logo grob.
setZeroBin Get and set the zero bin manually