# Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

## Documentation for package ‘Motif2Site’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

Bed2Granges | Read a bed file as Genomic Ranges
combine2Table | Combine all IP and Input count table files
combineMotifFiles | Combine motif bed files into a combined ranges
combineTestResults | Combine count Table and statistics table
compareBedFiless2UserProvidedRegions | Compare a set of bed files to a user provided regions set
CompareBeds2GivenRegions | Compare a set of bed files to a provided regions set
CompareMotifs2GivenRegions | Comparison motifs locations to a given regions set
compareMotifs2UserProvidedRegions | Compare a set of motifs to a user provided regions set
computeFoldEnrichment | compute fold enrichment values for an experiment
data | Synthetic datasets used in the package
decomposeBindingSignal | Decompose binding signal among accepted motifs
DeleteMultipleFiles | Delete a vector of files
deriveHeuristicBindingDistribution | build heurisitc distribution around the binding sites
DetectBindingSites | Detect binding sites from motif
DetectBindingSitesBed | Detect binding sites from bed motif input
DetectBindingSitesMotif | Detect binding sites from sequence motif sequence and mismatchNumber
DetectFdrCutoffBH | FDR cut-off detection Benjamini Hochberg method
findMotifs | Find motif instances with a certain mismatch number
fitKernelDensity | Fit a kernel density distribution to the obersever heuristic distribution
generate1ntBedAlignment | Convert bam and bed files to 1 nucleotide bed
Motif2Site | Detect and Recenter binding sites from ChIP-seq experiments
motifBindingNegativeBinomialCount | Model IP and Input count values with negative Binomal
motifChipCount | count short reads related to each motif for a given ChIPseq file
motifCount | count short reads around motifs for all ChIP-seq experiments
motifTablePreProcess | Process count data and perform negative binomial test
NegativeBinomialTestWithReplicate | Negative binomial test of binding using all replicates
pairwisDifferential | Detect differential motifs
quiet | Suppress messages generated by in external package
recenterBindingSitesAcrossExperiments | Combine binding sites across experiments
removeNonBellShapedMotifs | Remove non-bell shpape motifs prior to binding signal decomposition
strongestMotif | Returns the motif with the highest count