connected_component

Two samples are directly connected if they share at least one quantified fragment ion.
Two samples in a connected component are either directly connected or indirectly via other samples.

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

connected_component function

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

Arguments

Author

Group connected samples — connected_component

<dl>

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

</dl>

connected_component: Group connected samples

Description

Usage

Value

Arguments

Author

References