process_matrix: Process individual matrix

In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

Process individual matrix

Description

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

Usage

process_matrix(X, 
               method, 
               p1 = NULL, p2 = NULL, k = 1.345, min_M = 15, n_threads = -1)

Arguments

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

Value

A numeric row vector.

Author(s)

Thang V. Pham

References

Pham TV, Tran CTM, Henneman AA, Pham LHC, Le DG, Can AH, Bui PHL, Piersma SR, Jimenez CR. Boosting the speed and accuracy of protein quantification algorithms in mass spectrometry-based proteomics. Journal of Proteome Research 2026 Feb 6; 25(2):1198–1203.

iq documentation built on Oct. 28, 2026, 1:07 a.m.