getIBDpclusters: Genome Cluster Networks

In bahlolab/isoRelate: Identity-by-Descent Inference of Haploid Recombining Organisms

Description

getIBDpclusters() produces a network of clusters of isolates that share a minimum proportion of genome IBD. Isolates that do not share a minimum proportion IBD are not included in the network or output. The networks are created using R package igraph.

Usage

getIBDpclusters(ped.genotypes, ibd.segments, prop = 1, hi.clust = FALSE)

Arguments

ped.genotypes	A list containing 2 objects. See the Value description in getGenotypes for more details on this input.
ibd.segments	A data frame containing the IBD segments detected by isoRelate. See the Value description in getIBDsegments for more details on this input.
prop	Numeric value between (0,1]. The minimum proportion of genome shared IBD between a pair of isolates in order for the pair to be included in the network. For example, if prop=1 then two isolates will be included if they are IBD over the entire genome, i.e. identical isolates, whereas prop=0.5 will include isolates that share at least 50% of their genome IBD. The default is prop=1.
hi.clust	Logical. Whether to perform hierarchical clustering using the fastgreedy.community approach in the igraph package.

Value

A list of three objects named clusters, i.network and hi.clust:

1. A list where each object contains the names of isolates that form a disjoint cluster in the network. If hierarchical clustering has been performed then the clusters may not be disjoint.

2. An igraph network used in the construction of network plots. See http://igraph.org/r/ doe more details.

3. Logical. Whether or not hierarchical clustering has been performed.

See Also

getGenotypes, getIBDsegments and getIBDiclusters.

bahlolab/isoRelate documentation built on May 11, 2019, 5:25 p.m.