manyLoopPlots: Plot several loop regions

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

Description

manyLoopPlots takes a loops object and creates a time-stamped .pdf file with loop plots (one per page) of all regions specified in the GRanges object.

Usage

manyLoopPlots(x, y, organism = "h", geneinfo = "NA", colorLoops = FALSE,
  cache = TRUE, maxCounts = -1, showAnchorWidths = FALSE)

## S4 method for signature 'loops,GRanges'
manyLoopPlots(x, y, organism = "h",
  geneinfo = "NA", colorLoops = FALSE, cache = TRUE, maxCounts = -1,
  showAnchorWidths = FALSE)

Arguments

x	loops object
y	GRanges object with many regions to be visualized
organism	'h' for human or 'm' for mouse supported
geneinfo	A data.frame manually specifying annotation (see Examples)
colorLoops	Differentiates loops based on loop.type in loops object
cache	logic variable (default = TRUE) to use gene annotation from July.2015 freeze
maxCounts	Number of counts associated with thickest loop. Default is largest count in region displayed
showAnchorWidths	Display the width of the anchor on the plot? Default = FALSE

Details

Each plot will show one region sequentially that is supplied in the GRanges object.

Value

Prints a time stamped .pdf file of top loops

Examples

rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
jpn.u <- removeSelfLoops(loops.small)
assoc <- loopAssoc(jpn.u, coef = 2)
#manyLoopPlots(assoc, regs) #define regs as multiple GRanges

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.