create_snp_table: Create a SNP table

In maialab/daeqtlr: DAEQTL Mapping

Create a SNP table

Description

This function assembles a data frame of all SNPs involved in the DAEQTL mapping. Besides the genomic position for each SNP, it annotates each SNP as a DAE SNP or a DAEQTL candidate SNP: columns is_dae_snp and is_candidate_snp.

The returned data frame is useful as an intermediate data structure of the workflow, namely when looking for candidate neighbouring SNPs. Check the vignette('snp-pairs') to understand when to use this function.

Usage

create_snp_table(snp_gen_pos, dae_snps, candidate_snps)

Arguments

snp_gen_pos	A data frame of three columns: snp, chromosome and position.
dae_snps	A data frame of one column containing the DAE SNPs.
candidate_snps	A data frame of one column containing the DAEQTL candidate SNPs.

Value

This function adds two columns to snp_gen_pos in-place, so the object passed in snp_gen_pos will be modified after the call to this function.

maialab/daeqtlr documentation built on May 18, 2022, 6:53 a.m.