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, 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 March 21, 2026, 5:07 p.m.