computeFDR: Compute FDR given a score

In protViz/prozor: Minimal Protein Set Explaining Peptide Spectrum Matches

Compute FDR given a score

Description

Same as computeFDRwithID but works with decoy_hit boolean vector. For more details and references see package vignette vignette("TargetDecoyFDR_Example", package = "prozor")

Usage

computeFDR(score, decoy_hit, larger_better = TRUE)

Arguments

score	score
decoy_hit	indicates if decoy hit
larger_better	is larger score the better one (default TRUE)

Value

list with decoy_hit (indicates if decoy), score the search engine score, FDR1 false discovery rate estimated using the method of Gygi, SimpleFDR - estimated using the method of Kaell.

Examples

data(fdrSample)

fdr1 <- computeFDR(fdrSample$score, grepl("REV_",fdrSample$proteinID), larger_better = FALSE)
head(as.data.frame(fdr1))

protViz/prozor documentation built on Nov. 13, 2024, 12:30 a.m.