graph_clusters: Generate a graph from integrations sites within a specified...
In cnobles/gintools: Genomic DNA Integration Analysis Tools

Description Usage Arguments Details Author(s) Examples

Given a set of integration sites, this function generates a partial undirected graph of integration sites where nodes are the specific sites (one row from the GRanges object input) and edges mark which sites are within the gap distance from eachother. To generate the partial graph, nodes are broken into two groups, axil nodes and nodes. Axil nodes are the first occurances (or left most occurance) of the unique integration sites (chromsome + strand + position) which cluster together. Nodes are all other occurances, which are always connected to one axil node by definition.

1	graph_clusters(sites, gap)

`sites`	a GRanges object where each row is a single integration site or range.
`gap`	an integer specifying the distance to consider between sites to call an edge.

graph_clusters generates a partial undirected graph connecting each integration sites within a specified genomic gap distance.

Christopher Nobles, Ph.D.

sites <- GRanges(
  seqnames = rep("chr1", 7),
  ranges = IRanges(
    start = c(50, 49, 44, 50, 50, 50, 60),
    width = seq(20, 26, 1)),
  strand = rep("+", 7))

graph <- graph_clusters(sites, gap = 5L)

plot.igraph(graph)