write_primary_QC_report.SBA: Write primary QC report

In Rundmus/BAf-R_package: Binder Array data hanlding package in facility

Description

Write a primary QC report for SBA data using Rmarkdown

Usage

write_primary_QC_report.SBA(
  baf,
  bead_count = NULL,
  sample_order = order(batch(baf, "sample")),
  file = "primary_QC_report.html",
  title = paste("Primary QC report of", deparse(substitute(baf))),
  author = "Mun-Gwan",
  date = Sys.Date(),
  rm_Rmd = T,
  color_tbl_b = default_color_SBA_bead(T),
  color_tbl_s = default_color_SBA_ctrl_samples(sid(baf)),
  lowbound_mfi = 100
)

Arguments

baf	an object of the BAf-class that contains SBA data
bead_count	1) a data.frame, 2) a file name or 3) a matrix. check plot_QC_bead_count_boxplot
sample_order	the order of sample in plots. The default is the order by sample batch in order to easily check batch differences.
file	The name of the generating HTML file. The ".html" extension will be added if it is missing.
title	The title of the generating report, which is displayed at the top
author	The author of the report
date	The date written as the creation date
rm_Rmd	if the .Rmd (RMarkdown) file should be removed after .pdf was generated.
color_tbl_b	the colors of the binders employed for positive or negative control on plot. The information should be provided as a data.frame, in which columns are name, reg (regular expression to find the binder), col (color), and type (positive , negative, or measure). If this is given as NULL, it results in no coloring.
color_tbl_s	colors of samples on the plot. The information should be provided as a data.frame that has name, reg (regular expression to find the sample), col (color), type (negative or replicated). If this is NULL, then no coloring is applied.
lowbound_mfi	the lower bound of MFI. If a median of a sample is below this threshold, the data of the sample is neglected afterwords in this QC report.

Author(s)

Mun-Gwan Hong, [e-mail]

Rundmus/BAf-R_package documentation built on May 18, 2020, 12:59 p.m.