Replace protein-level quantifications with NA if they derive from too few lower feature level quantifications

Protein level abundances are more accurately quantified where there are more features (PSMs/peptides) to summarise from.

Usually, we are performing the summarisation from a matrix (columns=samples, rows=features) with an associated feature to protein ID mapping. Within the matrix, some values may be missing (NA). In order to correctly identify which proteins can be quantified, we need to start from the feature level object and create a mask which we can use to replace protein-level quantification values with NA. This is can be obtained with get_protein_no_quant_mask . This can then be combined with this function to replace protein level quantification values with NA where they were derived from too few quantification values

Usage

mask_protein_level_quant(obj, retain_mask)

Arguments

obj

SummarizedExperiment with PSM or peptide-level quantification

retain_mask

matrix detailing whether a protein-level quantification had sufficient lower level quantification values for each sample. Can be obtained with get_protein_no_quant_mask

Value

SummarizedExperiment with quantification values replaced by NA where they derive from too few lower feature level quantifications