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Wrapper for iq::maxLFQ to use with QFeatures::aggregateFeatures

maxlfq_wrapper.Rd

This function wraps iq::maxLFQ() so it can be passed to QFeatures::aggregateFeatures() as the fun argument. It expects a numeric matrix with peptides as rows and samples as columns, and returns a numeric vector of protein-level intensities.

Usage

maxlfq_wrapper(mat, ...)

Arguments

mat

A numeric matrix of peptide intensities (rows = peptides, columns = samples). Missing values should be NA.

...

Additional arguments passed to iq::maxLFQ().

Value

A numeric vector of length equal to the number of columns in mat, containing protein-level abundance estimates.

Details

The MaxLFQ algorithm computes protein abundances from peptide intensities by using peptide ratios across samples and solving a least-squares system. This wrapper extracts the estimate component returned by iq::maxLFQ() and coerces it to a numeric vector, suitable for aggregateFeatures().

Examples

if (FALSE) { # \dontrun{
library(QFeatures)
library(iq)

# Example peptide-level matrix (log2 intensities)
mat <- matrix(rnorm(20), nrow = 5, ncol = 4)
colnames(mat) <- paste0("Sample", 1:4)
rownames(mat) <- paste0("Pep", 1:5)

protein_estimates <- maxlfq_wrapper(mat)
} # }