In maialab/daeqtlr: DAEQTL Mapping

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(daeqtlr)

If your starting point for DAEQTL mapping is not the triad of the three data objects introduced in vignette('daeqtlr') and you need to assemble the set of SNP pairs for DAEQTL testing first, then this vignette is for you.

Here we show how to assemble a table of SNP pairs starting from:

• a list of DAE SNPs
• a list of candidate SNPs
• genomic positional annotation for those SNPs

Let us read in the three data sets above from the example files bundled with this {daeqtlr}:

dae_snps <- read_dae_snps(file = daeqtlr_example("dae_snps.txt"))
dae_snps[1:10, ]

candidate_snps <-
  read_candidate_snps(file = daeqtlr_example("candidate_snps.txt"))
candidate_snps[1:10, ]

snp_gen_positions <-
  read_snp_gen_positions(file = daeqtlr_example("snp_gen_positions.csv"))
snp_gen_positions[1:10, ]

We start by creating an intermediate data table (snp_table) with all the SNPs involved and their genomic positions, as well as the indication of who is a DAE SNP and who is a candidate SNP (they can be both). For that we use the function create_snp_table():

snp_table <-
  create_snp_table(snp_gen_pos = snp_gen_positions,
                   dae_snps = dae_snps,
                   candidate_snps = candidate_snps)
snp_table

To create the set of SNP pairs, we use the function create_snp_pairs() that takes in the snp_table. Essentially, the create_snp_pairs() searches within a genomic neighborhood of each DAE SNP for other SNPs marked as candidate SNPs. This genomic neighborhood is specified via a genomic window size centered on the DAE SNP. The window size defaults to 500 kb (window_size = 500000L), meaning a total of 1 Mb around the DAE SNP's position (500 kb to each side).

# Assembles a data table of SNP pairs
snp_pairs <- create_snp_pairs(snp_table = snp_table)

snp_pairs

And there you have it, the SNP pairs needed for DAEQTL mapping as explained in vignette('daeqtlr').

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