cisTrans: Identify x-y cis and trans edges.

In topherconley/spacemap: A novel conditional graphical model for integrative genomics

Description

Label igraph object with cis/trans status for x-y edges.

Usage

cisTrans(ig, level = c("x-y"), cw = 2e+06, ignoreStrand = TRUE)

Arguments

ig	An igraph network object output from rankHub
level	Character vector currently only supporting 'x-y' edge labeling of cis/trans status.
cw	Numeric value denoting the half length of the genomic interval used for calling a response node (i.e. of levels y) as cis regulated by a predictor node (i.e. of levels x). Defaults to 2Mb.
ignoreStrand	Logical defaults to TRUE specifying that strand specificity is not required to call cis/trans edges.

Details

This function requires the GenomicRanges package from Bioconductor. See http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html for installation details. The specific functions from GenomicRanges are 'findOverlaps' and 'countOverlaps'. The ig network parameter requires vertex attributes for genome coordinates specified as chr,start,end (see details section of adj2igraph).

Value

The igraph object ig with x-y edges updated with attribute 'cis_trans' indicating cis/trans status.

Also x node vertices are updated with attributes 'ntrans' reporting the number of trans regulations by a node (similarly for attribute 'ncis') and 'regulates_in_cis' lists specific y nodes regulated in cis by x nodes.

See Also

rankHub, adj2igraph, reportHubs, xHubEnrich

topherconley/spacemap documentation built on May 31, 2019, 6:36 p.m.