R: Compute FDR from posterior error probabilities PEP

computeFDR {scp}

R Documentation

Compute FDR from posterior error probabilities PEP

Description

The functions takes the posterior error probabilities (PEPs) from the given assay's rowData and adds a new variable to it (called .FDR) that contains the computed false discovery rates (FDRs).

Usage

computeFDR(object, i, groupCol, pepCol)

Arguments

`object`	A `QFeatures` object
`i`	A `numeric()` or `character()` vector indicating from which assays the `rowData` should be taken.
`groupCol`	A `character(1)` indicating the variable names in the `rowData` that contains the grouping variable. The FDR are usually computed for PSMs grouped by peptide ID.
`pepCol`	A `character(1)` indicating the variable names in the `rowData` that contains the PEPs. Since, PEPs are probabilities, the variable must be contained in (0, 1).

Value

A QFeatures object.

Examples

data("scp1")
scp1 <- computeFDR(scp1,
                   i = 1,
                   groupCol = "Sequence",
                   pepCol = "dart_PEP")
## Check results
rowDataToDF(scp1, 1, c("dart_PEP", ".FDR"))

[Package scp version 1.0.0 Index]