knit_see_gem_from_table: Knit SeeGEM from tidy data

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

Description

Create the interactive html document from a data frame / tibble

Usage

  knit_see_gem_from_table(rmd = system.file("rmd/document_template_from_table.Rmd",
  package = "SeeGEM"), output_file = "SeeGEM_document.html",
  output_directory = getwd(), table_data, sample_name = NA,
  title = "SeeGEM Test Report")

Arguments

rmd	Path to a custom R markdown file. A default R markdown file is provided with this package
output_file	Output name (I recommend ending in 'html', as this is what the file is) of your output file.
output_directory	Directory the output file will be written to. Defaults to your working directory.
table_data	Data frame (or tibble) to be knit
sample_name	The name of your sample
title	The title of the document

Value

None

Examples

## Not run: 
# will output just the example document to ~/SeeGEM_document.html
knit_see_gem()
# more realistic example which does an automsal recessive test 
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')

## End(Not run)

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