ipfReassignFDR {DIAlignR} | R Documentation

## Re-Assign FDR Aligned Peaks

### Description

This method will re-assign peaks with either the MS2 FDR if there was not enough confidence (identifying transitions) in the IPF FDR, or it will assign the user defined alignedFDR2. This assumes the reference run has a really good peak that meets the IPF FDR threshold.

### Usage

    ipfReassignFDR(dt, refRuns, fileInfo, params)

### Arguments

`dt` | (data.table) Aligned results tables from writeTables
`refRuns` | (dataframe) A peptide reference run table from getRefRun
`fileInfo` | (dataframe) A table with run filename information from getRunNames
`params` | (list) A list of parameters used by DIAlignR generated from paramsDIAlignR

### Value

(data.table) Aligned results table with reassigned m-scores

### Author(s)

Justin Sing, justinc.sing@mail.utoronto.ca

ORCID: 0000-0003-0386-0092

License: (c) Author (2020) + GPL-3 Date: 2020-07-17

### See Also

writeTables, getRefRun, getRunNames, paramsDIAlignR

### Examples

    ## Not run:
    finalTbl <- ipfReassignFDR(finalTbl, refRuns, fileInfo, params)

    ## End(Not run)

[Package DIAlignR version 2.2.0 Index]