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.