create_protein_table: Protein quantification for a list of proteins

In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

Protein quantification for a list of proteins

Description

Travels through the input list and quantifies all proteins one by one.

Usage

create_protein_table(protein_list, method = "maxLFQ", ...)

Arguments

protein_list	The input protein list
method	Possible values are "maxLFQ", "median_polish", "topN", and "meanInt".
...	Additional parameters for individual quantitation methods.

Value

A list of two components is returned

estimate	A table of protein abundances for all samples in log2 space.
annotation	A vector of annotations, one for each protein.

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.

See Also

create_protein_list, maxLFQ, median_polish, topN, meanInt

Examples

data("spikeins")
# This example set of spike-in proteins has been 'median-normalized'.
norm_data <- iq::preprocess(spikeins, median_normalization = FALSE, pdf_out = NULL)
protein_list <- iq::create_protein_list(norm_data)
result <- iq::create_protein_table(protein_list)
head(result)

iq documentation built on March 31, 2023, 11:34 p.m.