load_ibd_network

load_ibd_network

Usage

load_ibd_network(
  ibd_file,
  meta_file,
  ibd_co = c(0, 2, 1, 0),
  frac_co = 0.7,
  filter_on_meta = FALSE
)

Arguments

ibd_file

TSV file with IBD data

meta_file

TSV with node metadata

ibd_co

vector of cutoffs for defining an edge

frac_co

cutoff for quality control - default is 0.49

filter_on_meta

if true, only include edges that have nodes in meta df

Value

IBD network

Examples

ibd_file <- fs::path_package(
  "extdata",
  "example-ibd-data.tsv",
  package = "spIBDerverse"
)
meta_file <- fs::path_package(
  "extdata",
  "example-meta-data.tsv",
  package = "spIBDerverse"
)
load_ibd_network(
  ibd_file,
  meta_file,
  ibd_co = c(0, 2, 1, 0)
)
#> IGRAPH eb3f090 UN-- 328 1712 -- 
#> + attr: name (v/c), frac_gp (v/n), frac_missing (v/n), frac_het (v/n),
#> | n_cov_snp (v/n), Archaeological_ID (v/c), Master_ID (v/c), Projects
#> | (v/c), Locality (v/c), Province (v/c), Country (v/c), Latitude (v/n),
#> | Longitude (v/n), date (v/c), date_type (v/c), imputation_type (v/c),
#> | degree (v/n), closeness (v/n), betweenness (v/n), eigencentrality
#> | (v/n), frac_gp1 (e/n), frac_gp2 (e/n), max_ibd (e/n), sum_ibd_8
#> | (e/n), n_ibd_8 (e/n), sum_ibd_12 (e/n), n_ibd_12 (e/n), sum_ibd_16
#> | (e/n), n_ibd_16 (e/n), sum_ibd_20 (e/n), n_ibd_20 (e/n), wij (e/n)
#> + edges from eb3f090 (vertex names):
#> [1] KUP007--KUP023 RKC013--RKC029 RKC031--RKF238 RKF195--RKF196 RKC020--RKF142
#> + ... omitted several edges