filter_msgf_data: Filtering MSGF Data

In vladpetyuk/PlexedPiper: Pipeline for isobaric quantification.

Description

Filtering MSGF data. In this implementation the peptide level filter optimizes both ppm and PepQValue thresholds to achieve maximum number of peptide identifications within given FDR constrain.

Usage

filter_msgf_data(
  msnid,
  level,
  fdr.max = 0.01,
  n.iter.grid = 500,
  n.iter.nm = 100
)

Arguments

msnid	(MSnID object) collated MSGF output
level	(character) Level at which to perform FDR filter
fdr.max	(numeric) Maximum acceptable FDR rate. Default is 0.01.
n.iter.grid	(numeric) number of grid-distributed evaluation points. Default 500.
n.iter.nm	(numeric) number of iterations for Nelder-Mead optimization algorithm. Default 100.

Value

(MSnID object) filtered MSGF output

Examples

path_to_MSGF_results <- system.file("extdata/global/msgf_output", package = "PlexedPiperTestData")
msnid <- read_msgf_data(path_to_MSGF_results)
msnid <- MSnID::correct_peak_selection(msnid)
show(msnid)
msnid <- filter_msgf_data(msnid, "peptide", 0.01) # 1% FDR at peptide level
show(msnid)
path_to_FASTA <- system.file("extdata/Rattus_norvegicus_NCBI_RefSeq_2018-04-10.fasta.gz", package = "PlexedPiperTestData")
msnid <- compute_num_peptides_per_1000aa(msnid, path_to_FASTA)
msnid <- filter_msgf_data(msnid, "accession", 0.01) # 1% FDR at protein level
show(msnid)

vladpetyuk/PlexedPiper documentation built on June 24, 2021, 8:59 a.m.