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, 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.