maxLFQ {iq}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.


[Package iq version 1.9.12 Index]