Man pages for VplotR
Set of tools to make V-plots and compute footprint profiles

ABF1_sacCer3ABF1_sacCer3
alignToTSSA function to re-align a GRanges object to TSSs
ATAC_ce11_Serizay2020ATAC_ce11_Serizay2020
bam_testbam_test
ce11_all_REsce11_all_REs
ce11_promsce11_proms
computeNucleosomeEnrichmentOverBackgroundInternal function
computeVmatA function to compute Vplot matrix
CTCF_hg38CTCF_hg38
deconvolveBidirectionalPromotersA function to duplicate bi-directional GRanges
getCutsInternal function
getFragmentsDistributionA function to compute sizes distribution for paired-end...
importPEBamFilesA function to import paired end bam files as GRanges
MNase_sacCer3_Henikoff2011MNase_sacCer3_Henikoff2011
MNase_sacCer3_Henikoff2011_subsetMNase_sacCer3_Henikoff2011_subset
normalizeVmatA function to normalized a Vmat
nucleosomeEnrichmentA function to compute nucleosome enrichment over a set of...
nucleosomeEnrichment.GRangesA function to compute nucleosome enrichment over a set of...
nucleosomeEnrichment.VmatA function to compute nucleosome enrichment over a Vmat
plotFootprintA function to plot footprint of paired-end data at given loci
plotProfileA function to generate a Vplot along chromosome coordinates
plotVmatA function to generate a Vplot
plotVmat.defaultA function to plot a computed Vmat
plotVmat.GRangesA function to compute (and plot) a Vmat
plotVmat.listA function to compute (and plot) several Vmats.
plotVmat.VmatA function to plot a computed Vmat
plotVmat.VmatListA function to plot a computed VmatList
REB1_sacCer3REB1_sacCer3
sampleGRangesA function to sample GRanges from GRanges
sampleGRanges.GRangesA function to sample GRanges within GRanges
shiftATACGrangesA function to shift GRanges fragments by 5/-4. This is useful...
shuffleVmatA function to shuffle a Vmat
theme_ggplot2Personal ggplot2 theming function, adapted from...
VplotR documentation built on Nov. 8, 2020, 7:50 p.m.