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.