Package index • monaLisa

monaLisa package overview

monaLisa-package monaLisa: monaLisa - MOtif aNAlysis with Lisa.

Binned motif-enrichment analysis

Bin regions of interest and analyse motifs enrichments in bins.

bin(): Bin elements of x.
getZeroBin() setZeroBin(): Get and set the zero bin manually
calcBinnedMotifEnrR(): Binned Motif Enrichment Analysis with monaLisa
calcBinnedMotifEnrHomer(): Prepare and run HOMER motif enrichment analysis.
plotBinDiagnostics(): Plot diagnostics of binned sequences
plotBinDensity(): Density plot of binned elements.
plotBinHist(): Histogram of binned elements.
plotBinScatter(): Scatter plot (xy-plot) of binned elements.
plotMotifHeatmaps(): Heatmap of motif enrichments.

K-mer analysis

Functions for analysing word (k-mer) occurrences in sequences.

getKmerFreq(): Calculate observed and expected k-mer frequencies
calcBinnedKmerEnr(): Calculate k-mer enrichment in bins of sequences.

Identify predictive motifs using stability selection

Functions for selecting motifs that explain observed changes using Stability Selection.

randLassoStabSel(): Randomized Lasso Stability Selection
plotSelectionProb(): Plot selection probabilities of predictors
plotStabilityPaths(): Plot Stability Paths

Miscellaneous

Various utilites and helper functions, typically used in the functions above.

findMotifHits(): Find motif matches in sequences.
annoSeqlogo(): Sequence logo annotation
dumpJaspar(): Dump Jaspar motifs into a HOMER motif file.
homerToPFMatrixList(): Read a HOMER motif file and create a PFMatrixList
findHomer(): Find HOMER script file.
prepareHomer(): Prepare input files for HOMER motif enrichment analysis.
parseHomerOutput(): Load output from HOMER findMotifsGenome.pl into R
motifSimilarity(): Calculate similarities between pairs of motifs.
motifKmerSimilarity(): Calculate similarities between motifs and k-mers.
seqLogoGrob(): Create a simple sequence logo grob.
getColsByBin(): Get colors by bin.
sampleRandomRegions(): Sample random regions of fixed length.