check_snp_agreement: Agreement of SNPs

In hhhh5/ewastools: EWAS Tools

Agreement of SNPs

Description

These function check the agreement of genetic fingerprints between samples (after genotype calling with call_genotypes). In case of check_snp_agreement, the user supplies for each sample the assumed donor ID and the function returns all conflicts (i.d., either samples that are supposed to come from the same donor but have distinct genetic fingerprints or samples from supposedly different donors with the same fingerprints). check_snp_agreement on the other hand is inferring donor IDs in case they are unknown (useful for example to detect technical replicates in a public dataset).

Usage

check_snp_agreement(genotypes, donor_ids, sample_ids)

agreement_(genotypes, donor_ids, sample_ids, ...)

enumerate_sample_donors(genotypes)

Arguments

genotypes	Output of call_genotypes
donor_ids	Vector of donor IDs, should include duplicates
sample_ids	Vector of unique sample IDs

Value

check_snp_agreement returns all conflicts found between user-supplied donor IDs and those derived from the genetic fingerprint. Either NULL if not conflicts were found, or a list of data.tables, each representing one connected component of the conflict graph.

enumerate_sample_donors returns for each sample the donor IDs.

Author(s)

Jonathan A. Heiss

hhhh5/ewastools documentation built on Feb. 7, 2024, 6:21 p.m.