ARA: Aggregate Region Analysis

In jianhong/trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

Aggregate Region Analysis

Description

Extract the interaction signal means from given coordinates.

Usage

ARA(gr, upstream = 2e+05, downstream = upstream, resolution = 10000, ...)

Arguments

gr	A 'GRanges' object. The center of the object will be used for alignment for all the given regions.
upstream, downstream	numeric(1L). Upstream and downstream from the center of given 'gr' input will be used to extract the signals.
resolution	numeric(1L). The resolution will be passed to importGInteractions function.
...	The parameters used by importGInteractions function. Please note that the ranges resolution and out parameter should not be involved.

Value

A GInteractions object with scores which represent the mean values of the interactions.

Examples

hic <- system.file("extdata", "test_chr22.hic", package = "trackViewer",
                   mustWork=TRUE)
gr <- GRanges("22", c(seq(20000001, 50000001, by=10000000), width=1))
gi <- ARA(gr, file=hic, format="hic")
rg <- GRanges("22", IRanges(1, 400000))
op <- optimizeStyle(trackList(gi2track(gi)))
heatmap <- op$tracks
sty <- op$style
setTrackViewerStyleParam(sty, "xat", c(1, 200000, 400000))
setTrackViewerStyleParam(sty, "xlabel",c("-20K", "center", "20K"))
viewTracks(heatmap, viewerStyle=sty, gr=rg)

jianhong/trackViewer documentation built on March 17, 2024, 2:16 p.m.