create_protein_list {iq}

Creating a list of matrices of fragment ion intensities for all proteins

Description

For each protein, a numerical matrix is formed where the columns are samples and rows are fragment ions.

Usage

create_protein_list(preprocessed_data)

Arguments

preprocessed_data

A data frame of four components as output of the preprocess function.

Value

A list where each element contains the quantitative data of a protein. The column names are sample names and the row names fragment ions.

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

preprocess

Examples

data("spikeins")
head(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)