ipfReassignFDR: Re-Assign FDR Aligned Peaks

In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

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, [e-mail]

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)

shubham1637/DIAlignR documentation built on March 29, 2023, 8:45 p.m.