plot_ContUserScore: Plot Andromeda score distribution of contaminant peptide vs....
In PTXQC: Quality Report Generation for MaxQuant and mzTab Results

plot_ContUserScore

R Documentation

Plot Andromeda score distribution of contaminant peptide vs. matrix peptides.

Description

The data is expected to be an ECDF already, x being the Andromeda score, y being the culmulative probability. The Score is the probability of a Kolm.-Smirnoff test that the contaminant scores are larger (i.e. large p-values indicate true contamination). You will only see this plot if the but high-scoring contaminant peptides, which would erroneously give you a large p-value and make you believe your sample is contaminated although that's not the case.

Usage

plot_ContUserScore(data, raw.file, score)

Arguments

`data`	A data.frame with columns 'x', 'y', 'condition'
`raw.file`	Name of Raw file for which the data is displayed (will become part of the plot title)
`score`	Score of how distinct the distributions are (will become part of the title)

Value

GGplot object

Examples


 data = data.frame(x = 10:60,
                   y = c(seq(0,1,length=51), seq(0.1, 1, length=51)), 
                   condition = rep(c("sample","contaminant"), each=51))
 plot_ContUserScore(data, 'test file', 0.96)

PTXQC documentation built on May 29, 2024, 9:26 a.m.