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Load an IBD network

Source: R/load_ibd_network.R
load_ibd_network.Rd

Reads pairwise IBD data and node metadata, keeps pairs that pass the frac_gp quality filter and the IBD segment-count cutoffs, and builds an undirected igraph object weighted by sum_ibd_8.

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

Path to a TSV or CSV file with pairwise IBD data. Must contain iid1, iid2, n_ibd_8, n_ibd_12, n_ibd_16, n_ibd_20 and sum_ibd_8 (after janitor::clean_names()).

meta_file

Path to a TSV or CSV file with node metadata. If there is no iid column, the first column is used as the node ID. Must contain frac_gp if the IBD file lacks frac_gp1 and frac_gp2.

ibd_co

Numeric vector of length 4: minimum values of n_ibd_8, n_ibd_12, n_ibd_16 and n_ibd_20 required to define an edge.

frac_co

Quality-control cutoff; both nodes of a pair must have frac_gp >= frac_co. Default is 0.7.

filter_on_meta

If TRUE, only keep edges whose two nodes are both present in the metadata.

Value

An undirected igraph object with centrality measures added, or NULL (with a message) if the inputs cannot be read or are invalid.

Details

Input files can be tab-separated (.tsv, .tab, .txt) or comma-separated (.csv), optionally compressed (e.g. .csv.gz). The format is chosen from the file extension; for any other extension the delimiter is guessed from the file contents.

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 b89bb0d 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 b89bb0d (vertex names):
#> [1] KUP007--KUP023 RKC013--RKC029 RKC031--RKF238 RKF195--RKF196 RKC020--RKF142
#> + ... omitted several edges