decoyScoreTable: Prepare score table for decoys

In statOmics/TargetDecoy: Diagnostic Plots to Evaluate the Target Decoy Approach

Prepare score table for decoys

Description

Takes an input object and returns a score table for the decoys.

Usage

decoyScoreTable(object, decoy, score, log10 = TRUE)

Arguments

object	A data.frame, mzID or mzRident object.
decoy	character, name of the variable that indicates if the peptide matches to a target or to a decoy. When this value is missing, a Shiny gadget is launched to select it interactively.
score	numeric, indicating the score of the peptide match, obtained by the search engine. When this value is missing, a Shiny gadget is launched to select it interactively.
log10	logical to indicate if the score should be -log10-transformed. Default: TRUE. When this value is missing, a Shiny gadget is launched to select it interactively.

Value

A data.frame with a logical "decoy" column and numeric "scores".

Author(s)

Elke Debrie, Lieven Clement

Examples

library(mzID)

## Use one of the example files in the mzID package
exampleFile <- system.file("extdata", "55merge_tandem.mzid", package = "mzID")
mzIDexample <- mzID(exampleFile)

decoyScoreTable(mzIDexample, decoy = "isdecoy", score = "x\\!tandem:expect")

statOmics/TargetDecoy documentation built on Nov. 9, 2022, 9:30 a.m.