plotTopLoops {diffloop} | R Documentation

## 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)

    ## 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)

[Package diffloop version 1.18.0 Index]