In protViz/TargetDecoyFDR: Compute False Discovery Rates Given Score and Target Decoy Information

knitr::opts_chunk$set(
  echo = TRUE,
  message = FALSE,
  warning = FALSE
)

The data

The package provides sample data. The data needs to have two columns, one with a label, to distinguish targets and decoys, the other with a score. Then you also need to know if a larger score or a smaller score is better. In our example data, we have two scores: score and score2. While the score is better if it smaller, score2 is better if it is larger.

rm(list=ls())
library(dplyr)
library(TargetDecoyFDR)
data(fdrSample)
x <-dplyr::arrange(fdrSample, score2)
library(TargetDecoyFDR)
knitr::kable(head(fdrSample))

What is also required is that the number of Targets and Decoys are the same. This is usually given for mass spectrometry database searches. Our dataset here is truncated already at a 5% FDR. Therefore the number of decoys is much smaller.

table(grepl("REV_",fdrSample$proteinID))

In our example, we will use the package to filter the data further for a 1% FDR.

Computing the FDR can be done by calling the function computeFDR. plotFDR than shows the score distribution for the targets (black) and decoys (red) as well as the FDR for each score (x axis).

fdr1 <- computeFDR(fdrSample$score, grepl("REV_",fdrSample$proteinID),larger_better = FALSE)
plotFDR(fdr1)

The output is a named list which can be easily converted into a data frame. We next will briefly discuss the elements of the output.

knitr::kable(head(data.frame(fdr1)))

The order column

Since the scores are sorted to compute the FDR, we return also the order column. This column can be used to align the ID's with the scores.

knitr::kable(head(data.frame(ID = fdrSample$proteinID[fdr1$order], fdr1)))

For convinience we provide the function computeFDRwithID which integrates the reordering of the ID's.

fdr1 <- computeFDRwithID(fdrSample$score,fdrSample$proteinID, decoy = "REV_",larger_better = FALSE)
knitr::kable(head(data.frame(fdr1)))

Types of FDR

There are various types of measures in result dataframe.

We define here

 * FP as the number of passing decoy assignments
 * TP as the number of passing forward hits.

The the false postive rate is given by:

$$ FPR = \frac{2 \cdot FP}{TP + FP} $$ The multiplier 2 is needed here since we assume that also the forward sequences have false assignments.

This is taken from the reference by [@Elias2007].

"The FDR associated with a particular score threshold is defined as the expected percentage of accepted PSMs that are incorrect, where an accepted PSM is one that scores above the threshold (Many proteomics papers incorrectly refer to this quantity as the false positive rate)." ([@Kaell2007])

The Simple FDR intrudced by ([@Kaell2007]) is defined by :

$$ SimpleFDR = \frac{FP}{TP} $$

"For a given score threshold, we count the number of decoy PSMs above the threshold and the number of target PSMs above the threshold. We can now estimate the FDR by simply computing the ratio of these two values (SimpleFDR)."[@Kaell2007]

plot(fdr1$score, fdr1$SimpleFDR, type="l", xlim=c(0,0.002), ylim=c(0,0.0005))
lines(fdr1$score, fdr1$qValue_SimpleFDR, col=3, type="l", xlim=c(0,0.002), ylim=c(-0.002,0))

Because of this, although the score is getting better (smaller) the FDR may increase since the number of TP in the denominator decreases while the number of FP stays the same. Therefore Storey and Tibshirani proposed the q-value, "which in our case is defined as the minimal FDR threshold at which a given PSM is accepted"[@Kaell2007].

Getting the score for an FDR.

Most frequently you will need to get the score for an FDR in order to filter your data. To report your data with an FDR of 1% instead of 5% you can execute this code:

names(fdr1)

(score01G <- predictScoreFDR(fdr1,qValue = 5,method = "FPR"))
dim(dplyr::filter(fdrSample, score < score01G))

(score01G <- predictScoreFDR(fdr1,qValue = 1,method = "FPR"))
dim(dplyr::filter(fdrSample, score < score01G))

(score01K <- predictScoreFDR(fdr1,qValue = 1,method = "SimpleFDR"))
dim(dplyr::filter(fdrSample, score < score01K))

References

protViz/TargetDecoyFDR documentation built on May 26, 2019, 9:37 a.m.