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)
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