diffloop (version 1.0.2)

plotTopLoops: Plot the most significant loops

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)
## S3 method for class '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

Value

• Prints a time stamped .pdf file of top loops

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.)

Examples

rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
jpn.u <- removeSelfLoops(loops.small)
jpn_loopfit <- loopFit(jpn.u)
assoc_jn <- loopTest(jpn_loopfit, coef = 2)
plotTopLoops(assoc_jn, n=2)