ScoreInAlignWindow

Using the result from 'alignmentCheck()', score the features of every Raw file and see if they 
have been properly aligned.
Returned value is between 0 (bad) and 1 (all aligned).

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

ScoreInAlignWindow function

<dl><dt>data</dt>
<dd>A data.frame with columns 'rtdiff' and 'raw.file'</dd>
<dt>allowed.deltaRT</dt>
<dd>The allowed matching difference (1 minute by default)</dd></dl>

Arguments

Compute the fraction of features per Raw file which have an acceptable RT difference after alignment — ScoreInAlignWindow

<dl>

<dt>data</dt>
<dd>A data.frame with columns 'rtdiff' and 'raw.file'</dd>


<dt>allowed.deltaRT</dt>
<dd>The allowed matching difference (1 minute by default)</dd>

</dl>

ScoreInAlignWindow: Compute the fraction of features per Raw file which have an acceptable RT difference after alignment

Description

Usage

Value

Arguments