Glossary

Key Points

Introduction	An expression quantitative trait locus (eQTL) explains part of the variation in gene expression. Traditional linkage and association mapping can be applied to gene expression traits (transcripts). Genetic variants, such as single nucleotide polymorphisms (SNPs), that underlie eQTL illuminate transcriptional regulation and variation.
Genetic Drivers of Pancreatic Islet Function	. .
Load and explore the data
Review Mapping Steps	To understand the key steps running a QTL mapping analysis
Mapping A Single Gene Expression Trait	To run a QTL analysis for expression data
Mapping Many Gene Expression Traits
Creating A Transcriptome Map	Transcriptome maps aid in understanding gene expression regulation.
Transcriptome Map of cis and trans eQTL	.
Maximum eQTL Peaks and Nearby Genes	.
Interpreting qtl2 results	Edit the .Rmd files not the .md files
Mediation Analysis	Mediation analysis investigates an intermediary between an independent variable and its effect on a dependent variable. Mediation analysis is used in high-throughput genomics studies to identify molecular phenotypes, such as gene expression or methylation traits, that mediate the effect of genetic variation on disease phenotypes or other outcomes of interest.

association mapping: scanning the genome for significant associations between genetic markers (e.g. SNPs) and phenotypes to identify functional genetic variants (e.g. loci or alleles) linkage disequilibrium; frequency of association between loci is non-random and is higher or lower than would be expected if they were independent and randomly associated; alleles tend to co-segregate and be inherited together in LD
linkage mapping; determining the position of genes or genetic markers relative to one another on the same chromosome by the recombination frequency between them