plot.fdr_table {SWATH2stats} | R Documentation

## Plot functionality for results of class "fdr_table" as produced by e.g. the function assess_fdr_overall()

### Description

This function created standard plots from results of class "fdr_table" as produced by e.g. the function assess_fdr_overall() visualizig ID numbers in dependence of estimated FDR and also estimated FDR in dependence of m_score cutoff.

### Usage

    ## S3 method for class 'fdr_table'
    plot(x, output = "Rconsole", filename = "FDR_report_overall", ...)

### Arguments

`x` | List of class "fdr_table" as produced e.g. by the function assess_fdr_overall() from this package.
`output` | Choose output type. "pdf_csv" creates the output as files in the working directory, "Rconsole" triggers delivery of the output to the console enabling further computation or custom plotting / output.
`filename` | Basename for output files to be created (if output = "pdf_csv" has been selected).
`...` | further arguments passed to method.

### Value

Plots in Rconsole or report files.

### Author(s)

Moritz Heusel

### Examples

    data("OpenSWATH_data", package="SWATH2stats")
    data("Study_design", package="SWATH2stats")
    data <- sample_annotation(OpenSWATH_data, Study_design)
    x <- assess_fdr_overall(data, FFT=0.7, output = "Rconsole", plot = FALSE)
    plot.fdr_table(x, output = "pdf_csv", filename = "Assess_fdr_overall_testplot")

[Package SWATH2stats version 1.16.0 Index]