List of Metrics"
In 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.