assembleMZQC

Collects all 'mzQC' members from each entry in lst_qcMetrics and stores them in an overall mzQC object, which can be written to disk (see writeMZQC()) or augmented otherwise

Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015)
<doi:10.1021/acs.jproteome.5b00780>.

Chris Bielow

PTXQC

Quality Report Generation for MaxQuant and mzTab Results

Juliane Schmachtenberg

Swenja Wagner

Patricia Scheil

Tom Waschischek

Guido Mastrobuoni

assembleMZQC function

<dl><dt>lst_qcMetrics</dt>
<dd>A list of qcMetric objects which have their mzQC member populated with "MzQCrunQuality" and/or "MzQCsetQuality" objects</dd>
<dt>raw_file_mapping</dt>
<dd>A data.frame with cols 'from', to' and maybe 'best.effort' (if shorting was unsuccessful), as e.g. obtained by a FilenameMapper$raw_file_mapping</dd></dl>

Arguments

Collects all 'mzQC' members from each entry in lst_qcMetrics and stores them in an overall mzQC object, which can be written to disk (see writeMZQC()) or augmented otherwise — assembleMZQC

<dl>

<dt>lst_qcMetrics</dt>
<dd>A list of qcMetric objects which have their mzQC member populated with "MzQCrunQuality" and/or "MzQCsetQuality" objects</dd>


<dt>raw_file_mapping</dt>
<dd>A data.frame with cols 'from', to' and maybe 'best.effort' (if shorting was unsuccessful), as e.g. obtained by a FilenameMapper$raw_file_mapping</dd>

</dl>

Collects all 'mzQC' members from each entry in lst_qcMetrics and stores them in an overall mzQC object, which can be written to disk (see writeMZQC()) or augmented otherwise

assembleMZQC: Collects all 'mzQC' members from each entry in lst_qcMetrics and stores them in an overall mzQC object, which can be written to disk (see writeMZQC()) or augmented otherwise

Description

Usage

Value

Arguments