Calculate iBAQ values from raw intensities

Calculate iBAQ values from raw intensities

Usage

calculate_iBAQ(pr_matrix, ibaq_stats = NULL, organism = "hs")

Arguments

pr_matrix

The report.pr_matrix file

ibaq_stats

Dataframe with proteinIDs and associated number of iBAQ peptides obtained with get_ibaq_peptides. Required when not using pre-calculated iBAQ peptides

organism

Specifies which organism to use if using pre-calculated iBAQ peptides. 'hs' for human, 'mm' for mouse.

Value

A dataframe with iBAQ values per proteinGroup per sample and the number of iBAQ peptides.

Examples

ibaq_values <- calculate_iBAQ(report.pr_matrix, organism = 'hs') # For human
ibaq_values <- calculate_iBAQ(report.pr_matrix, organism = 'mm') # For mouse