In dmgatti/qtl2med: Mediation Analysis for qtl2

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

Setup

library(qtl2med)

Use a locus on Chr 13 near 112.2 Mb as the mediation locus.

build = 90
chr = 13
pos = 112.205823
cc_dbfile = "C:/Users/dgatti/Documents/Sanger/cc_variants.sqlite"

Get Ensembl genes for one chormosome from a specific Ensembl build.

ensembl = get_ensembl_genes(chr = chr, build = build)

Mediate using founder allele probabilities.

med_allele = mediate(pheno = pheno,
                     chr = chr,
                     pos = pos,
                     type = "haplo",
                     expr = expr,
                     ensembl = ensembl,
                     genoprobs = genoprobs,
                     addcovar = addcovar)

Plot the mediation scan on Chr 13, labelling all genes that are more than 6 standard deviations from the mean LOD score.

plot_med(med = med_allele, threshold = 6)

Mediate using the SNP probabilities.

med_snp = mediate(pheno = pheno,
                  chr = chr,
                  pos = pos,
                  type = "snp",
                  expr = expr,
                  ensembl = ensembl,
                  genoprobs = genoprobs,
                  addcovar = addcovar,
                  cc_dbfile = cc_dbfile)

plot_med(med = med_snp, threshold = 6)

Additional functions that may be used, if needed.

Get founder allele probs near a given position.

gp = get_allele_probs(chr = chr, pos = pos, genoprobs = genoprobs, map = map)

Get SNP probs near a given position.

query_fxn = qtl2::create_variant_query_func(cc_dbfile, filter = "type=='snp'")
sp = get_snp_probs(chr = chr, pos = pos, genoprobs = genoprobs,
                   map = map, query_fxn = query_fxn)