tag_mendelian_incompatibilities: Identify loci in PO pairs that are Mendelian incompatible

In eriqande/CKMRsim: Inference of Pairwise Relationships Using Likelihood Ratios

Identify loci in PO pairs that are Mendelian incompatible

Description

This is a handy function for taking parent-offspring pairs, typically identified using CKMRsim, and then tagging the loci at which the observed/recorded genotypes are not compatible with Mendelian inheritance. This version is currently very simple and merely looks at pairs of individuals. (i.e., it does not attempt to identify Mendelian incompatible loci on the basis of pa-ma-kid trios.) Noetheless, it should be useful for identifying poor-performing loci.

Usage

tag_mendelian_incompatibilities(po, geno)

Arguments

po

a tibble of the parent-offspring pairs. This will typically be obtained by filtering the output for pairwise_kin_logl_ratios() and it must have the format of that output: columns of D2_indiv, D1_indiv, logl_ratio, and num_loc.

geno

a long format data frame / tibble of genotype data for both the candidate offspring and the candidate parents. Typically this is what you get if you use bind_rows() on the D1 and D2 inputs to pairwise_kin_logl_ratios() for a parent-offspring type of analysis. Must have the columns: Indiv, Locus, gene_copy, and Allele. Obviously, the IDs in Indiv must correspond to those used in D1_indiv and D2_indiv

Details

Note that if you want to count up the relative frequency (across all pairs) of Mendelian incompatibilities at each locus you can do like this:

tag_mendelian_incompatibilities(po, geno) %>%
 group_by(Locus) %>%
 summarise(mean_incompat = mean(is_MI, na.rm = TRUE)) %>%
 arrange(desc(mean_incompat))

Value

This returns a tibble with the columns:

• D2_indiv: the ID of the D2_indiv

• D1_indiv: the ID of the D1_indiv

• logl_ratio: the log-likelihood ratio for parent-offspring for the pair

• Locus: the name of the locus

• ⁠D1a_1, D1a_2, D2a_1, D2a_2⁠: D1_indiv's allelic type of gene copy 1 and 2, and then D2_indiv's allelic type of gene copy 1 and 2, respectively

• is_MI: logical vector. TRUE if the pair is Mendelian incompatible at the Locus. Otherwise FALSE (or NA if either member of pair was NA)

eriqande/CKMRsim documentation built on Aug. 2, 2024, 7:23 a.m.