fast_MaxLFQ

A fast implementation of the MaxLFQ algorithm.

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

fast_MaxLFQ function

<dl> <dt>norm_data</dt>
<dd>A list of four vectors with equal length <code>protein_list</code>, <code>sample_list</code>, <code>id</code> and <code>quant</code> as prepared by the <code>fast_preprocess</code> function or the <code>quant_table</code> component returned by the <code>fast_read</code> function. Note that <code>quant</code> should contain log2 intensities.</dd> <dt>row_names</dt>
<dd>A vector of character strings for row names. If <code>NULL</code>, unique values in the <code>protein_list</code> component of <code>norm_data</code> will be used. Otherwise, it should be the first column of the <code>protein</code> component returned by the <code>fast_read</code>.</dd> <dt>col_names</dt>
<dd>A vector of character strings for column names. If <code>NULL</code>, unique values in the <code>sample_list</code> component of <code>norm_data</code> will be used. Otherwise, it should be the <code>sample</code> component returned by the <code>fast_read</code>.</dd></dl>

Arguments

Author

The MaxLFQ algorithm — fast_MaxLFQ

<dl>

 <dt>norm_data</dt>
<dd>A list of four vectors with equal length <code>protein_list</code>, <code>sample_list</code>, <code>id</code> and <code>quant</code> as prepared by the <code>fast_preprocess</code> function or the <code>quant_table</code> component returned by the <code>fast_read</code> function. Note that <code>quant</code> should contain log2 intensities.</dd>

 <dt>row_names</dt>
<dd>A vector of character strings for row names. If <code>NULL</code>, unique values in the <code>protein_list</code> component of <code>norm_data</code> will be used. Otherwise, it should be the first column of the <code>protein</code> component returned by the <code>fast_read</code>.</dd>

 <dt>col_names</dt>
<dd>A vector of character strings for column names. If <code>NULL</code>, unique values in the <code>sample_list</code> component of <code>norm_data</code> will be used. Otherwise, it should be the <code>sample</code> component returned by the <code>fast_read</code>.</dd>

</dl>

fast_MaxLFQ: The MaxLFQ algorithm

Description

Usage

Value

Arguments

Author

References

See Also