process_matrix

Estimates a row vector best representing all rows in the input numeric matrix.

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,
the median polish algorithm by Tukey (1977, ISBN:0201076160), and a robust linear model.
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

process_matrix function

<dl> <dt>X</dt>
<dd>A matrix of intensities in the log2 space. Columns are samples and rows are fragment ions.</dd> <dt>method</dt>
<dd>One of the quantification methods: <code>"maxlfq"</code>, <code>"maxlfq_bit"</code>, 
 <code>"weighted_maxlfq"</code>, <code>"median_polish"</code>, <code>"weighted_median_polish"</code>, <code>"rlm"</code>, 
 or <code>"weighted_rlm"</code>.</dd> <dt>p1</dt>
<dd>Method parameter. For <code>"rlm"</code> and <code>"weighted_rlm"</code>, it is the robust parameter. 
 For <code>"median_polish"</code> and <code>"weighted_median_polish"</code>, it is the convergence parameter. Unused in other cases.</dd> <dt>p2</dt>
<dd>Method parameter. For <code>"maxlfq_bit", it specifies the memory level. For others, it is the maximum number of optimization rounds.</code></dd> <dt>k</dt>
<dd>Weighting function parameter.</dd> <dt>min_M</dt>
<dd>Minimum number of rows for the weighted methods.</dd> <dt>n_threads</dt>
<dd>The number of threads to be used. When <code>n_threads</code> is 0, the maximal number of CPU cores is used. 
 When <code>n_threads</code> is -1 (default), one CPU core less than the maximum is used, and so on.</dd></dl>

Arguments

Author

Process individual matrix — process_matrix

<dl>

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

 <dt>method</dt>
<dd>One of the quantification methods: <code>"maxlfq"</code>, <code>"maxlfq_bit"</code>, 
 <code>"weighted_maxlfq"</code>, <code>"median_polish"</code>, <code>"weighted_median_polish"</code>, <code>"rlm"</code>, 
 or <code>"weighted_rlm"</code>.</dd>

 <dt>p1</dt>
<dd>Method parameter. For <code>"rlm"</code> and <code>"weighted_rlm"</code>, it is the robust parameter. 
 For <code>"median_polish"</code> and <code>"weighted_median_polish"</code>, it is the convergence parameter. Unused in other cases.</dd>

 <dt>p2</dt>
<dd>Method parameter. For <code>"maxlfq_bit", it specifies the memory level. For others, it is the maximum number of optimization rounds.</code></dd>

 <dt>k</dt>
<dd>Weighting function parameter.</dd>

 <dt>min_M</dt>
<dd>Minimum number of rows for the weighted methods.</dd>

 <dt>n_threads</dt>
<dd>The number of threads to be used. When <code>n_threads</code> is 0, the maximal number of CPU cores is used. 
 When <code>n_threads</code> is -1 (default), one CPU core less than the maximum is used, and so on.</dd>

</dl>

process_matrix: Process individual matrix

Description

Usage

Value

Arguments

Author

References