plotTopLoops: Plot the most significant loops

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

Description

plotTopLoops takes a loops object and creates a time-stamped .pdf file with loop plots (one per page) of the top loops.

Usage

plotTopLoops(lto, n = 0, PValue = 1, FDR = 1, organism = "h",
  colorLoops = FALSE)

## S4 method for signature 'loops'
plotTopLoops(lto, n = 0, PValue = 1, FDR = 1,
  organism = "h", colorLoops = FALSE)

Arguments

lto	loops object
n	number of loops to print (can remain 0 to specify from other parameters) determined by PValue
PValue	Maximum pvalue threshold for loop inclusion when printing loop plot
FDR	False discovery rate threshold for inclusion
organism	Either 'm' for mouse or 'h' for human.
colorLoops	Default FALSE; specify true if rowData slot contains loop.type from annotateLoops to visualize plots with varying colors for CTCF looping and enhancer-promoter looping

Details

Each plot will show the region +/- 1 loopwidth of the loop with annotation specified for either human or mouse. Assumes columns Pvalue and FDR are specified in the loops object. We recommend removing self loops before using this function (and in reality, before any association testing was called.)

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)
plotTopLoops(assoc, n=2)

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