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()
#> processing file: document_template.Rmd
#> output file: document_template.knit.md
#> /usr/local/bin/pandoc +RTS -K512m -RTS document_template.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output /Users/mcgaugheyd/SeeGEM_document.html --email-obfuscation none --self-contained --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:flatly' --include-in-header /var/folders/s4/y5f1tt296dj8088gvczcx11d4lrnr7/T//RtmpnsOXEh/rmarkdown-str2bcc415bf54b.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
#> 
#> Output created: ~/SeeGEM_document.html

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')
#> processing file: document_template.Rmd
#> output file: document_template.knit.md
#> /usr/local/bin/pandoc +RTS -K512m -RTS document_template.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output /Users/mcgaugheyd/SeeGEM_document.html --email-obfuscation none --self-contained --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:flatly' --include-in-header /var/folders/s4/y5f1tt296dj8088gvczcx11d4lrnr7/T//RtmpnsOXEh/rmarkdown-str2bcc29c4120a.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
#> 
#> Output created: ~/SeeGEM_document.html

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 or functions to call gemini from R and pull the data into the function.

It is much simpler to use the since it has pre-filled out sensible default filters (see the documentation). You just need need to feed 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 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.