# Analysis tools for Single Molecule Footprinting (SMF) data

## Documentation for package ‘SingleMoleculeFootprinting’ version 1.12.0

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

## Help Pages

BaitCapture | Bait capture efficiency
BinMethylation | Summarize methylation inside sorting bins
CallContextMethylation | Call Context Methylation
CollapseStrands | Collapse strands
CollapseStrandsSM | Collapse strands in single molecule matrix
ConversionRate | Conversion rate
CoverageFilter | Filter Cs for coverage
DetectExperimentType | Detect type of experiment
FilterByConversionRate | Calculate reads conversion rate
FilterContextCytosines | Filter Cytosines in context
FixOverhang | Fixing overhang before stand collapsing
GetQuasRprj | Get QuasRprj
GetSingleMolMethMat | Get Single Molecule methylation matrix
HierarchicalClustering | Perform Hierarchical clustering on single reads
OneTFstates | Design states for single TF case
PlotAvgSMF | Plot average methylation
PlotSingleMoleculeStack | Plot single molecule stack
PlotSingleSiteSMF | Plot SMF data at single site
PlotSM | Wrapper for PlotSingleMoleculeStack function
SampleCorrelation | Intersample correlation
SingleTFStateQuantificationPlot | Single TF state quantification bar
SortReads | Sort reads by single TF
SortReadsBySingleTF | Wrapper to SortReads for single TF case
SortReadsByTFCluster | Wrapper to SortReads for TF cluster case
StateQuantificationPlot | Plot states quantification bar
TFPairStateQuantificationPlot | TF pair state quantification bar
TFpairStates | Design states for TF pair case