merge_genotypes_with_annotation: Merge genotypes with annotation

In santiago1234/phdpopgene: What the Package Does (One Line, Title Case)

Description

Merges the genotypes with the annotation (FUNSEQ and Consequences) and puts the table in long format. This function also removes all sites, for each individual-sample, that are homozygous (0|0) since these sites don't contribute to the load.

Usage

merge_genotypes_with_annotation(genotipos, annotation, h_samples)

Arguments

genotipos	the tidy genotypes, output of get_genotype
annotation	table with annotation, the output of get_var_annotation
h_samples	vector of samples, a subset of the samples

Value

A data frame, with the following columns

varid

Variant ID

Consequence

Variant consequence

FUNSEQ

funseq score

individual

individual id, example: HG00551

genotype

the genotype of the individual, example: 0|1

santiago1234/phdpopgene documentation built on Dec. 31, 2020, 5:06 a.m.