In davemcg/SeeGEM: Integrate 'GEMINI' (and 'peddy') Output into Interactive Html Document

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

Quick Start

The SeeGEM package contains the information used to create the demo file

Before you get started with your own data, I suggest you recreate this document to make sure you have all of the libraries and pandoc installed on your computer.

library(SeeGEM)
knit_see_gem()

This should create SeeGEM_document.html in your base user directory (~/)

To see an example of what the peddy integrated report looks like run this:

knit_see_gem(skip_stats = 'no')

Now it is time to use your own data. You will need the following:

1. GEMINI installed (e.g. if you go to your shell and type gemini it will run (with an error about too few arguments)
2. A GEMINI database

You can use the \code{\link{gemini_test_wrapper}} or \code{\link{gemini_query_wrapper}} functions to call gemini from R and pull the data into the \code{\link{knit_see_gem}} function.

It is much simpler to use the \code{\link{gemini_test_wrapper}} since it has pre-filled out sensible default filters (see the documentation). You just need need to feed \code{\link{gemini_test_wrapper}} the GEMINI database ('2018_06_28__OGVFB_exomes.GATK.PED_master.gemini.db'), the test you want to run ('autosomal_recessive'), finally the family that you want to return the results from ('DDL003').

Then give the path and name of the output file and tell \code{\link{knit_see_gem}} to use the use the no stats template with skip_stats = 'no'

knit_see_gem(GEMINI_data = gemini_test_wrapper('2018_06_28__OGVFB_exomes.GATK.PED_master.gemini.db', 
                                               test = 'autosomal_recessive', 
                                               families = 'DDL003'), 
             output_file='quick_SeeGEM.html', 
             skip_stats = 'yes')

Depending on the speed of the GEMINI query, this can create the document in seconds, potentially making it possible to use SeeGEM in an exploratory manner.

davemcg/SeeGEM documentation built on May 5, 2019, 1:34 a.m.