PPplot: Creates PP plot of two empirical distributions.

In compomics/search-all-assess-subset: An implementation of the Search All, Asses Subset strategy for FDR estimation shotgun proteomics.

Description

Creates PP plot of two empirical distributions.

Usage

PPplot(score, label, pi0 = 0, score_higher = TRUE,
  title = "PP plot of target PSMs", xlab = "Decoy percentile",
  ylab = "Target\npercentile")

Arguments

score	vector of quantiles of distribution 1 and 2
label	vector of logical values. TRUE if score belongs to distribution 1
pi0	mixture coefficient of distribution 1 in distribution 2
score_higher	TRUE if a higher score means a better PSM.
title	main title.
xlab	label on x-axis.
ylab	label on y-axis.

Value

ggplot object

Examples

## Simulate a dataset with 140 correct target subset PSMs, 60 incorrect target subset PSMS,
## 60 decoy subset PSMs and 2000 additional decoy PSMs.
set.seed(10)
d = sample_dataset(H1_n = 140,H0_n = 60, decoy_n = 60 ,decoy_large_n = 2000)

##pi_0 can be estimated with the target-decoy approach
pi0 = sum(d$decoy & d$subset)/sum(!d$decoy & d$subset)
PPplot(d$score, d$decoy, pi0)

compomics/search-all-assess-subset documentation built on May 13, 2019, 9:55 p.m.