reorganize_matching_samples: Relabel matching genotypes to a single ID and reorganize...

In eriqande/HatcheryPedAgree:

Relabel matching genotypes to a single ID and reorganize their years and spawner groups

Description

If there are matching samples, we want to make sure that we have just a single ID for each cluster, and that the years and spawner groups get organized so that SNPPIT can read all that information in.

Usage

reorganize_matching_samples(genotypes, metadata, clusters)

Arguments

genotypes	the genotypes
metadata	the metadata
clusters	the tibble with the matching sample clusters.

Value

A list with a variety of components:

• matchers_metadata: a tibble of all the matching sample clusters and their metadata

• snppit_meta: a tibble of metadata in long format that is preped for use in prepare_snppit_infile()

• snppit_genos: a tibble of genotype data in long format that is preped for use in prepare_snppit_infile()

• cross_hatchery_matches: a tibble of matching samples that were spawned at more than one hatchery

• cross_sex_matches: a tibble of matching samples that are marked as both sexes

• geno_discord: a list like that returned in count_discrepancies().

eriqande/HatcheryPedAgree documentation built on Sept. 21, 2023, 7:24 p.m.