s2s_all_filters: Gather together the various SWATH2stats filters into one...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Gather together the various SWATH2stats filters into one place.

Description

There are quite a few filters available in SWATH2stats. Reading the documentation, it seems at least possible, if not appropriate, to use them together when filtering DIA data before passing it to MSstats/etc. This function attempts to formalize and simplify that process.

Usage

s2s_all_filters(
  s2s_exp,
  column = "proteinname",
  pep_column = "fullpeptidename",
  fft = 0.7,
  plot = FALSE,
  target_fdr = 0.02,
  upper_fdr = 0.05,
  mscore = 0.01,
  percentage = 0.75,
  remove_decoys = TRUE,
  max_peptides = 15,
  min_peptides = 2,
  do_mscore = TRUE,
  do_freqobs = TRUE,
  do_fdr = TRUE,
  do_proteotypic = TRUE,
  do_peptide = TRUE,
  do_max = TRUE,
  do_min = TRUE,
  ...
)

Arguments

s2s_exp	SWHAT2stats result from the sample_annotation() function. (s2s_exp stands for: SWATH2stats experiment)
column	What column in the data contains the protein name?
pep_column	What column in the data contains the peptide name (not currently used, but it should be.)
fft	Ratio of false negatives to true positives, used by assess_by_fdr() and similar functions.
plot	Print plots of the various rates by sample?
target_fdr	When invoking mscore4assayfdr, choose an mscore which corresponds to this false discovery date.
upper_fdr	Used by filter_mscore_fdr() to choose the minimum threshold of identification confidence.
mscore	Mscore cutoff for the mscore filter.
percentage	Cutoff for the mscore_freqobs filter.
remove_decoys	Get rid of decoys in the final filter, if they were not already removed.
max_peptides	A maximum number of peptides filter.
min_peptides	A minimum number of peptides filter.
do_mscore	Perform the mscore filter? SWATH2stats::filter_mscore()
do_freqobs	Perform the mscore_freqobs filter? SWATH2stats::filter_mscore_freqobs()
do_fdr	Perform the fdr filter? SWATH2stats::filter_mscore_fdr()
do_proteotypic	Perform the proteotypic filter? SWATH2stats::filter_proteotypic_peptides()
do_peptide	Perform the single-peptide filter? SWATH2stats::filter_all_peptides()
do_max	Perform the maximum peptide filter? SWATH2stats::filter_max_peptides()
do_min	Perform the minimum peptide filter? SWATH2stats::filter_min_peptides()
...	Other arguments passed down to the filters.

Value

Smaller SWATH2stats data set.

See Also

[SWATH2stats]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.