# Analysis tools for Single Molecule Footprinting (SMF) data

## Documentation for package ‘SingleMoleculeFootprinting’ version 2.2.0

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

## Help Pages

.detect.footprints | Detects TF and nucleosome footprints enriched in a single partition
AggregateFootprints | Gather equivalent footprints by overlaps (and TF identity) under the same index
AnnotateFootprints | Annotate detected TF footprints with user-provided TF motif annotations
Arrange_TFBSs_clusters | Convenience function to arrange a list of given TFBSs into clusters
BaitCapture | Bait capture efficiency
BinMethylation | Summarize methylation inside sorting bins
CallContextMethylation | Call Context Methylation
cbind_fill_sparseMatrix | Implementation performing a similar operation of rbind_fill_sparseMatrix but for columns
CollapseStrands | Collapse strands
CollapseStrandsSM | Collapse strands in single molecule matrix
CollectCompositeData | Collect bulk SMF data for later composite plotting
colMeans_drop0 | Calculate colMeans after dropping zeros
CompositeMethylationCorrelation | Composite Methylation Rate
CompositePlot | Plot composite SMF data
ConversionRate | Conversion rate
CoverageFilter | Filter Cs for coverage
Create_MethylationCallingWindows | Create methylation calling windows to call context methylation in one run for clusters lying proximally to each other
DetectExperimentType | Detect type of experiment
DetectFootprints | Wrapper to run the function detect.footprint across all clusters computed over a single locus
fill.empty.columns | Fills empty columns
filter.dense.matrix | Filters dense matrix
FilterByConversionRate | Calculate reads conversion rate
FilterContextCytosines | Filter Cytosines in context
filter_reads_from_MethGR | Recalculate *_T and *_M values in MethGR object after filtering reads e.g. for conversion rate
FootprintCharter | Run FootprintCharter
full.join.granges | Utility function to perform the dplyr full_join operation on GRanges object
GetQuasRprj | Get QuasRprj
GetSingleMolMethMat | Get Single Molecule methylation matrix
GRanges_to_DF | Manipulate GRanges into data.frame
HierarchicalClustering | Perform Hierarchical clustering on single reads
LowCoverageMethRate_RMSE | Low Coverage Methylation Rate RMSE
MaskSNPs | Utility function to remove cytosines whose MTase target genomic context is affected by SNPs
matrix.sliding.window.average | Computes rolling mean
MethSM.to.dense | Turn sparse single molecule matrix to dense
MethSM.to.MethGR | Compute MethGR from MethSM
panel.cor | Utility for HighCoverage_MethRate_SampleCorrelation
panel.hist | Utility for HighCoverage_MethRate_SampleCorrelation
panel.jet | Utility for HighCoverage_MethRate_SampleCorrelation
PlotAvgSMF | Plot average methylation
PlotFootprints | Plot bulk SMF separately for each partition alognside footprint detection results.
PlotSingleMoleculeStack | Plot single molecule stack
PlotSingleSiteSMF | Plot SMF data at single site
PlotSM | Wrapper for PlotSingleMoleculeStack function
Plot_FootprintCharter_SM | Plot single molecule heatmaps of footprint detection results
Plot_LowCoverageMethRate | Plot low coverage methylation rate
Plot_LowCoverageMethRate_RMSE | Plot Low Coverage Methylation Rate RMSE
rbind_fill_sparseMatrix | Implementation performing a similar operation of the plyr function rbind.fill.matrix but for sparseMatrix
RollingMean | Compute rolling mean
rowMeans_drop0 | Calculate rowMeans after dropping zeros
SingleTFStateQuantificationPlot | Single TF state quantification bar
SingleTFStates | Hard-coded interpretation of biological states from single TF sorting
SortReads | Sort reads by single TF
SortReadsBySingleTF | Wrapper to SortReads for single TF case
SortReadsBySingleTF_MultiSiteWrapper | Convenience wrapper to sort single molecule according to TFBS clusters at multiple sites in the genome
SortReadsByTFCluster | Wrapper to SortReads for TF cluster case
SortReadsByTFCluster_MultiSiteWrapper | Convenience wrapper to sort single molecule according to TFBS clusters at multiple sites in the genome
StateQuantification | Convenience for calculating state frequencies
StateQuantificationBySingleTF | Convenience for calculating state frequencies after sorting reads by single TF
StateQuantificationByTFPair | Convenience for calculating state frequencies after sorting reads by TF pair
StateQuantificationPlot | Plot states quantification bar
SubsetGRangesForSamples | Subset Granges for given samples
TFPairStateQuantificationPlot | TF pair state quantification bar
TFPairStates | Design states for TF pair case