manyLoopPlots: Plot several loop regions

Description Usage Arguments Details Value Examples

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

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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

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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

Bioconductor-mirror/diffloop documentation built on June 1, 2017, 7:35 a.m.