Analysis tools for Single Molecule Footprinting (SMF) data

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Documentation for package ‘SingleMoleculeFootprinting’ version 2.3.1

• 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