summarize_pairs: Summarize extent of relatedness of intra- and inter-facility...

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

Summarize extent of relatedness of intra- and inter-facility pairs by facility pair

Description

Summarize extent of relatedness of intra- and inter-facility pairs by facility pair

Usage

summarize_pairs(pair_types, summary_fns = c("min"), threshs = seq(5, 20, 5))

Arguments

pair_types	the output object of the get_pair_types function
summary_fns	vector of summary functions for pairwise distances as character strings (default: c("min"))
threshs	SNV thresholds to use for pairwise distances (default: seq(5, 20, 5))

Value

a summary of isolate pairs between each facility pair. leq = less than or equal to

Examples

## Not run: 
locs <- metadata %>% dplyr::select(isolate_id, facility) %>% tibble::deframe()
pair_types <- get_pair_types(dists, locs)
summarize_pairs(pair_types = pair_types)

## End(Not run)

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