maxLFQ: The MaxLFQ algorithm for protein quantification
In iq: Protein Quantification in Mass Spectrometry-Based Proteomics
maxLFQ R Documentation
The MaxLFQ algorithm for protein quantification
Description
Estimates protein abundances by aiming to maintain the fragment intensity ratios between samples.
Usage
maxLFQ(X)
Arguments
X
A matrix of ion intensities in log2 space. Columns are samples and rows are fragment ions.
Value
A list of two components is returned
estimate
A vector with length equal to the number of columns of the input containing the protein abundances in log2 space.
annotation
An empty string if all quantified samples are connected. Otherwise, a string of membership of the connected components is returned.
Author(s)
Thang V. Pham
References
Cox J, Hein MY, Luber CA, et al. Accurate proteome-wide label-free quantification
by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.
Mol Cell Proteomics. 2014;13(9):2513–2526.
Pham TV, Henneman AA, Jimenez CR. iq: an R package to estimate relative protein
abundances from ion quantification in DIA-MS-based proteomics. Bioinformatics 2020 Apr 15;36(8):2611-2613.
iq documentation built on May 29, 2024, 8:40 a.m.
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| maxLFQ | R Documentation |
The MaxLFQ algorithm for protein quantification
Description
Estimates protein abundances by aiming to maintain the fragment intensity ratios between samples.
Usage
maxLFQ(X)
Arguments
X |
A matrix of ion intensities in log2 space. Columns are samples and rows are fragment ions. |
Value
A list of two components is returned
estimate |
A vector with length equal to the number of columns of the input containing the protein abundances in log2 space. |
annotation |
An empty string if all quantified samples are connected. Otherwise, a string of membership of the connected components is returned. |
Author(s)
Thang V. Pham
References
Cox J, Hein MY, Luber CA, et al. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics. 2014;13(9):2513–2526.
Pham TV, Henneman AA, Jimenez CR. iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics. Bioinformatics 2020 Apr 15;36(8):2611-2613.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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