get_clusters: Get facility clusters on the phylogeny

In Snitkin-Lab-Umich/regentrans: A framework and R package for using genomics to study regional pathogen transmission

Get facility clusters on the phylogeny

Description

Get facility clusters on the phylogeny

Usage

get_clusters(tr, locs, pureness = 1, bootstrap = NULL, pt)

Arguments

tr	a tree object returned by the read.tree function from the ape package
locs	a named vector of locations of isolates (e.g. facility of isolation), with the name being the sample ID
pureness	how pure each cluster should be (must be > 0.5) (optional, defauly = 1)
bootstrap	Bootstrap support to use to filter unconfident tree edges (optional, default = NULL)
pt	a named vector of patients each isolate originated from, with the name being the sample ID. If this information is unavailable, set pt = NULL.

Value

list where pure_subtree_info is a data.frame of facility clusters on phylogeny, index indicates which element that cluster is in the list of subtrees, NA indicates it is not part of a subtree; subtrees is an object of the actual subtrees (can be used for plotting); cluster_pureness is the purness of each cluster

Examples

## Not run: 
locs <- metadata %>% dplyr::select(isolate_id, facility) %>% tibble::deframe()
pt <- metadata %>% dplyr::select(isolate_id, patient_id) %>% tibble::deframe()
clusts <- get_clusters(tr, locs, pureness = 1, bootstrap = NULL, pt)

## End(Not run)

Snitkin-Lab-Umich/regentrans documentation built on Jan. 29, 2023, 7:45 a.m.