Function reference • VplotR

Fragment density plots
`computeVmat()`	A function to compute Vplot matrix
`normalizeVmat()`	A function to normalized a Vmat
`shuffleVmat()`	A function to shuffle a Vmat
Plotting functions
`plotFootprint()`	A function to plot footprint of paired-end data at given loci
`plotProfile()`	A function to generate a Vplot along chromosome coordinates
`plotVmat()`	A function to generate a Vplot
`plotVmat(<default>)`	A function to plot a computed Vmat
`plotVmat(<Vmat>)`	A function to plot a computed Vmat
`plotVmat(<VmatList>)`	A function to plot a computed VmatList
`plotVmat(<list>)`	A function to compute (and plot) several Vmats.
`plotVmat(<GRanges>)`	A function to compute (and plot) a Vmat
Nucleosome enrichment scores
`nucleosomeEnrichment()`	A function to compute nucleosome enrichment over a set of GRanges
`nucleosomeEnrichment(<GRanges>)`	A function to compute nucleosome enrichment over a set of GRanges
`nucleosomeEnrichment(<Vmat>)`	A function to compute nucleosome enrichment over a Vmat
Utilities
`getFragmentsDistribution()`	A function to compute sizes distribution for paired-end fragments
`importPEBamFiles()`	A function to import paired end bam files as GRanges
`shiftATACGranges()`	A function to shift GRanges fragments by 5/-4. This is useful when dealing with fragments coming from ATAC-seq.
`alignToTSS()`	A function to re-align a GRanges object to TSSs
`deconvolveBidirectionalPromoters()`	A function to duplicate bi-directional GRanges
`sampleGRanges()`	A function to sample GRanges from GRanges
`sampleGRanges(<GRanges>)`	A function to sample GRanges within GRanges
Data
`ATAC_ce11_Serizay2020`	ATAC_ce11_Serizay2020
`MNase_sacCer3_Henikoff2011`	MNase_sacCer3_Henikoff2011
`MNase_sacCer3_Henikoff2011_subset`	MNase_sacCer3_Henikoff2011_subset
`ce11_all_REs`	ce11_all_REs
`ce11_proms`	ce11_proms
`CTCF_hg38`	CTCF_hg38
`REB1_sacCer3`	REB1_sacCer3
`ABF1_sacCer3`	ABF1_sacCer3
`bam_test`	bam_test
Internal functions
`getCuts()`	Internal function
`computeNucleosomeEnrichmentOverBackground()`	Internal function
`theme_ggplot2()`	Personal ggplot2 theming function, adapted from roboto-condensed at https://github.com/hrbrmstr/hrbrthemes/

Reference

Fragment density plots

Plotting functions

Nucleosome enrichment scores

Utilities

Data

Internal functions