In byandell/qtl2shiny: Shiny interface for 'qtl2' Fine Mapping

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This document concerns a suite of packages complementary to R/qtl2 that extend capabilities in terms of plotting, fast data access, deeper probe of SNPs and structural variants, and a user-friendly interface for deep investigation of small intervals.

The QTL2 Shiny Interface can be invoked from the Shiny server http://www.statlab.wisc.edu/shiny/qtl2shiny. We demonstrate with a publicly available dataset from Recla (see https://github.com/rqtl/qtl2data). However, this Shiny server is set up with project-specific login and password protection for data that has not been published, using server side Apache htaccess.

Strategy to Study Small Interval

Here is a strategy to look at multiple traits in a small interval. These are rough and ready notes that will be smoothed out in time.

• use analyses table (or other approach) to identify region of interest
  • say 1-5Mb window
• identify set of traits in region
• estimate allele effects at peak for each trait
  • useful plots?
• find best SNP(s) and pattern(s)
  • identify SDP and pattern for each
  • useful plots?
• do same for full effects
  • 36 diplotypes
  • 3-level SNPs

Some challenges

• don't have useful thresholds yet
• would like to think about inference across related patterns
• multiple peaks in small region
• pleiotropy vs close linkage

How to incorporate this into shiny tool?

• quick computation: limit size of region
• do we have to run genome scan?
  • or just consider flanking markers for each peak?

QTL2 Shiny Interface

Information will appear here about how the Shiny Interface works.

R/qtl2 companion packages

The popular R/qtl package for gene mapping has been redeveloped for high volume, multi-parent systems genetics data as R/qtl2. This new package is still in a state of flux, so please work with us to improve.

This document describes companion packages that are used to build the Shiny server:

• R/qtl2ggplot
• R/qtl2feather
• R/qtl2pattern
• R/qtl2shiny

The three other packages can be employed on their own separate from the server. In particular, R/qtl2ggplot provides full capability for ggplot2 plot objects. The R/qtl2feather package transforms large, slow calc_genoprob objects central to R/qtl2 into a set of feather databases for quick access. See each package for its own documentation.

There is another package that is more specialized and still need documentation: R/CausalMST concerns Causal Model Selection Tests, which are used in conjunction with mediation to formally infer causal relationship between a phenotype and other phenotypes that co-map. Plan is to try to combine this with R/intermediate.

byandell/qtl2shiny documentation built on June 11, 2025, 4:54 a.m.