process_iq_format: Process data in the iq format
In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

process_iq_format

R Documentation

Process data in the iq format

Description

Estimates protein abundance of all proteins in the iq format data.

Usage

process_iq_format(input_data,
                  output_filename = NULL,
                  method = "maxlfq_bit", 
                  p1 = NULL, p2 = NULL, k = 1.345, min_M = 15, n_threads = -1,
                  rescale_method = NULL)

Arguments

`input_data`	Input data in the iq format.
`output_filename`	Output file name. If `NULL`, a file name derived from `input_data` will be used.
`method`	See `method` in `process_matrix`.
`p1`	See `p1` in `process_matrix`.
`p2`	See `p2` in `process_matrix`.
`k`	See `k` in `process_matrix`.
`min_M`	See `min_M` in `process_matrix`.
`n_threads`	See `n_threads` in `process_matrix`.
`rescale_method`	Rescale the output intensities. See `method` in `rescale`.

Value

A tab-separated table with rows representing proteins and columns representing protein annotations and samples.

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.