Label igraph object with cis/trans status for x-y edges.
cisTrans(ig, level = c("x-y"), cw = 2e+06, ignoreStrand = TRUE)
| ig | An igraph network object output from |
|---|---|
| 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. |
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.
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).