topN {iq}

The topN algorithm for protein quantification

Description

Estimates protein abundances using the N most intense ions.

Usage

topN(X, N = 3, aggregation_in_log_space = TRUE)

Arguments

X

A matrix of ion intensities in log2 space. Columns are samples and rows are fragment ions.

N

The number of top ions used for quantification.

aggregation_in_log_space

A logical value. If FALSE, data aggregation is performed in the original intensity space.

Value

A list of two components is returned

estimate

A vector with length equal to the number of columns of the input containing the protein abundances in log2 space.

annotation

Reserved, currently an empty string.

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.