knit_see_gem: Knit SeeGEM with peddy stats

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

Description

Create the interactive html document

Usage

knit_see_gem(rmd = system.file("rmd/document_template.Rmd", package =
  "SeeGEM"), output_file = "SeeGEM_document.html",
  output_directory = getwd(),
  GEMINI_data = system.file("extdata/GEMINI_data.Rdata", package =
  "SeeGEM"), sample_name = NA, title = "SeeGEM Test Report",
  peddy_path_prefix = paste0(system.file("extdata/", package = "SeeGEM"),
  "/SEE_GEM_PEDDY"), peddy_id = c("1045", "1046", "1265"),
  decorate = TRUE, skip_stats = "no")

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.
GEMINI_data	Path to .Rdata data frame which contains the Data Frame of the GEMINI output that will be plotted. Helper scripts are provided as gemini_test_wrapper and gemini_query_wrapper which will return the GEMINI output as a data frame into your R session.
sample_name	The name of your sample
title	The title of the document
peddy_path_prefix	Path and prefix for the peddy output
peddy_id	A character vector of the samples you want to highlight in the peddy QC tab
decorate	TRUE or FALSE. If set to TRUE (default), then the data frame given as input 'GEMINI_data' will be decorated with the default settings for See_GEM_formatter. If you have already run this function on the data frame you are giving to knit_see_gem, then set this to FALSE.
skip_stats	If set to 'yes' this will use an alternate template which has no 'peddy QC' tab.

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.