Hands On Session: exploring microhaplotypes with ‘microhaplot’

The R-package program microhaplot provides functionality to extract microhaplotypes from aligned reads in .sam files, and to display information about reads containing microhaplotypes in a variety of useful visualizations. The goals is to give users the chance to dig into the patterns in their data and assess the quality of data at different microhaplotype loci.

Installation

This R package can be installed from GitHub:

devtools::install_github("ngthomas/microhaplot", build_vignettes = TRUE)

Known issues

• If you are working on a mac and just upgraded to a new major version of R, you should also reinstall XQuartz.
• If you are working on windows and are using R 3.5.1, things won’t work out because microhaplot makes use of the feather package, which is currently not built for 3.5.1. :-(.

After installing some steps to launch it

You have to load the package, move the Shiny app materials to a good location and then launch the Shiny app:

# provide a directory path to host the haPLOType app
microhaplot::mvHaplotype("~/Shiny")

# launch the Shiny app:
library(microhaplot)
app.path <- "~/Shiny/microhaplot"
runHaplotype(app.path)

Now, you can follow along with the first vignette:

vignette("haPLOType-walkthrough")

If you want more background on preparing your data for microhaplot try this:

vignette("haPLOT-data-prep")

I will spend a little time showing a new feature that is mostly undocumented—the “Scatter Analysis,” which was suggested by Phil Morin, and is a great way of looking at the data.