describeProteins: Describe protein and peptide compositions

In rformassspectrometry/PSM: Handling and Managing Peptide Spectrum Matches

Describe protein and peptide compositions

Description

It is important to explore PSM results prior to any further downstream analysies. Two functions, that work on PSM() and ConnectedComponents() objects can be used for this:

• The describeProteins() function describe protein composition in terms of unique and shared peptides.

• The describePeptides() function describe unique/shared peptide composition.

Usage

describeProteins(object)

describePeptides(object)

Arguments

object

Either an instance of class Matrix, PSM() or ConnectedComponents().

Value

describePeptides() invisibly return the table of unique and shared peptides. describeProteins() invisibly returns a data.frame with logicals indicating the unique/shared peptide composition of proteins. Both functions are used for their side effects of printing a short descriptive output about peptides and proteins.

Examples

f <- msdata::ident(full.names = TRUE, pattern = "TMT")
basename(f)
psm <- PSM(f) |>
       filterPsmDecoy() |>
       filterPsmRank()

describePeptides(psm)
describeProteins(psm)

rformassspectrometry/PSM documentation built on March 20, 2024, 9:16 a.m.