Aggregate Region Analysis — ARA • trackViewer

Extract the interaction signal means from given coordinates.

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)