topN

Estimates protein abundances using the N most intense ions.

An implementation of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive
pipeline for processing proteomics data in data-independent acquisition mode
(Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>).
It offers additional options for protein quantification using
the N most intense fragment ions, using all fragment ions, and
a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
In general, the tool can be used to integrate multiple
proportional observations into a single quantitative value.

Thang Pham

Protein Quantification in Mass Spectrometry-Based Proteomics

Alex Henneman

topN function

<dl><dt>X</dt>
<dd>A matrix of ion intensities in log2 space. Columns are samples and rows are fragment ions.</dd><dt>N</dt>
<dd>The number of top ions used for quantification.</dd><dt>aggregation_in_log_space</dt>
<dd>A logical value. If <code>FALSE</code>, data aggregation is performed in the original intensity space.</dd></dl>

Arguments

Author

The topN algorithm for protein quantification — topN

<dl>

<dt>X</dt>
<dd>A matrix of ion intensities in log2 space. Columns are samples and rows are fragment ions.</dd>

<dt>N</dt>
<dd>The number of top ions used for quantification.</dd>

<dt>aggregation_in_log_space</dt>
<dd>A logical value. If <code>FALSE</code>, data aggregation is performed in the original intensity space.</dd>

</dl>

topN: The topN algorithm for protein quantification

Description

Usage

Value

Arguments

Author

References