inMatchWindow

A data.frame with columns 'fc.raw.file', 'rtdiff_mixed', 'rtdiff_genuine'

data

The allowed matching difference for each Raw file (as data.frame(fc.rawfile, m))

df.allowed.deltaRT

Looking at groups only: Compute the fraction of 3D-peak pair groups per Raw file which 
have an acceptable RT difference after alignment using the result from 'idTransferCheck()',
i.e. compute the fraction of groups which are within a certain RT tolerance.

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>.

inMatchWindow: For grouped peaks: separate them into in-width vs. out-width class.

Description

Usage

Arguments

Value

Details