estimateDecoyFDR: Estimate decoy based featureFinding FDR.

In CCprofiler/CCprofiler: Complex feature detection using SEC protein chromatograms.

Description

Estimate FDR statistics based on a decoy model after feature finding.

Usage

estimateDecoyFDR(features, FFT = 1, grid_search_params = NULL,
  verbose = TRUE)

Arguments

features	data.table containing filtered complex feature results.
FFT	Numeric, fraction of false targets. Only useful in special cases, should not be altered in a generic workflow. Defaults to 1.
grid_search_params	Character vector of columns to report with the statistics for the dataset. Usually only useful for a grid search. Otherwhise the default should not be altered. Default = NULL.
verbose	Logical, wether to print messages. Default = TRUE.

Value

List with stats

Examples

#-----------------------------
## Complex Features
#-----------------------------

## Load example data
complexFeatures <- exampleComplexFeatures
## Filter feature table 
complexFeaturesFiltered <- filterFeatures(complexFeatures,
                                          min_peak_corr= 0.5,
                                          min_feature_completeness= 0.5) 

## estimate the FDR
estimateDecoyFDR(complexFeaturesFiltered)

#-----------------------------
## Protein Features
#-----------------------------

## Load example data
proteinFeatures <-exampleProteinFeatures
## Filter feature table 
proteinFeaturesFiltered <- filterFeatures(proteinFeatures,
                                          min_peak_corr= 0.5,
                                          min_feature_completeness= 0.5) 

## estimate the FDR
estimateDecoyFDR(proteinFeaturesFiltered)

CCprofiler/CCprofiler documentation built on May 19, 2021, 7:40 p.m.