In cbielow/PTXQC: Quality Report Generation for MaxQuant and mzTab Results

## global options
knitr::opts_chunk$set(echo=FALSE, warning=FALSE, error=FALSE, message=FALSE, fig.width=10)

lst_qcMetrics_ord = PTXQC:::getMetricsObjects()

txt_TOC = "# Table of Contents
  - [Overview](#Overview)
  - [Metrics](#Metrics)
"
txt_BODY = ""
for (qcm in lst_qcMetrics_ord)
{
  newname = gsub("(.*)\\(.*" , "\\1", gsub("[\\*~%]" , " ", gsub("[\\^\">]" , "", qcm$qcName))) 
  ## remove weird symbols (to serve as link)
  newname_lnk = gsub("[^a-zA-Z0-9]", "", newname)
  txt_TOC = paste0(txt_TOC, paste0("    - [", newname, "](#", newname_lnk, ")\n"))
  txt_BODY = paste0(txt_BODY, '\n
## ', newname, ' <a name="', newname_lnk, '"/>
\n
  <div class="helpText">', qcm$helpTextTemplate, '</div>
<p style="text-align: right"><a href="#TOP">-- back to top --</a></p>\n\n')
}

## print the TOC
cat(txt_TOC)

Overview

The following metrics are implemented in PTXQC.

Reasons why metrics might not appear in every report

• applicable only to certain types of data, e.g. SILAC or TMT
• metric was disabled manually using the YAML config file
• missing input data (incomplete tables), i.e. some .txt files are missing

Metric names are prefixed by the data-source, e.g. "EVD: Charge" displays and scores the charge distribution, based on data from 'evidence.txt' (EVD).

• EVD: evidence.txt
• SM: summary.txt
• PAR: parameters.txt
• PG: proteingroups.txt
• MSMS: msms.txt
• MS2Scans: msmsscans.txt

Some metrics are incompletely named here, since they might contain (hithero unknown) thresholds, which are taken from mqpar.xml (when available) or defaulted in real reports.

Metrics

  cat(txt_BODY)

If the above list is empty, the vignette was not compiled (e.g. when viewing on GitHub). Please see https://CRAN.R-project.org/package=PTXQC --> Vignettes for a compiled version.

cbielow/PTXQC documentation built on March 13, 2024, 5:08 a.m.