In maialab/daeqtlr: DAEQTL Mapping

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daeqtlr

The goal of {daeqtlr} is to perform differential allelic expression trait loci (DAEQTL) mapping.

Differential allelic expression (DAE) can be treated as a quantitative trait. Marker genotypes collected from the same set of individuals can, in turn, be used in testing statistical associations with DAE. This package provides routines for performing such a workflow, i.e. DAEQTL mapping.

Learn more in https://maialab.org/daeqtlr.

Installation

You can install the development version of {daeqtlr} like so:

# install.packages("remotes")
remotes::install_github("maialab/daeqtlr")

Usage

Here's a quick example on how to perform DAEQTL mapping with {daeqtlr}. For more details about this example read vignette("daeqtlr").

library(daeqtlr)

# SNP pairs to be tested for statistical association
snp_pairs <- read_snp_pairs(file = daeqtlr_example("snp_pairs.csv"))

# Zygosity levels (homozygous or heterozygous) for genotyped SNPs
zygosity <- read_snp_zygosity(file = daeqtlr_example("zygosity.csv"))

# Allelic expression (AE) ratios of DAE SNPs
ae <- read_ae_ratios(file = daeqtlr_example("ae.csv"))

mapping_dt <-
  daeqtl_mapping(snp_pairs = snp_pairs,
                 zygosity = zygosity,
                 ae = ae)

# Here's the first 30 SNP pairs tested
mapping_dt[1:30, -c('dae_snp_position', 'candidate_snp_position')]