MSnID-class: The "MSnID" Class for Mass Spectrometry Based Proteomics...

In MSnID: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Description

The MSnID is a convenience class for manipulating the MS/MS search results.

Objects from the Class

The way to create objects is to call MSnID constructor function that takes as an input the project working directory workDir and the second argument if the cache from previous analysis should be cleaned cleanCache.

Slots

workDir:

Object of class "character". containing working directory for the project. The .Rcache subdirectory stores the cached resuls form the previous analyses. The mechanism of caching relies on R.cache package.

psms:

Object of class data.table that contains all the MS/MS identification results in the form of peptide(or protein)-spectrum-matches.

Methods

read_mzIDs

signature(object, mzids):
Reads mzIdentML files into psms data.table slot of object MSnID instance. The functionality leverage mzID package facility. Note, the calls are memoised using R.cache facility. So if the call with the same list of files issues again, the results will be read from cache instead of re-parsing the mzIdentML files. See read_mzIDs

psms(object), psms(object)<-value:

Gets and sets MS/MS search results as data.frame. See psms

dim

signature(x = "MSnID"):
Returns the dimensions of the table with MS/MS identification data.

peptides

signature(object = "MSnID"):
Returns unique peptide list. See peptides

accessions

signature(object = "MSnID"):
Returns unique accessions (typically proteins) list. See accessions

proteins

signature(object = "MSnID"):
Returns unique proteins list. See proteins

assess_termini

Checks the agreement of peptide termini with enzymes cleavage specificity. The return value is theMSnID object with extra variable numIrregCleavages. See assess_termini

assess_missed_cleavages

Checks if the peptide sequence contains the sites that were not cleaved by the enzyme. For details see assess_missed_cleavages

mass_measurement_error

Returns parent ion mass measurement error in parts per million (ppm) units. Note, it requires experimentalMassToCharge and calculatedMassToCharge variables to be set. See mass_measurement_error

recalibrate

Recalibrates, that is removes systematic error from experimentalMassToCharge measurements. See recalibrate

correct_peak_selection

Subtracts or adds the mass difference between C13 and C12 isotopes (1.0033548378 Da) if that reduces the mass error. Such a mass error arises from the fact that instrument may peak non-monoisotopic peak for fragmentation and thus report the mass that is different by ~ 1 Da. See correct_peak_selection

apply_filter

signature(msnidObj="MSnID", filterObj="character")
signature(msnidObj="MSnID", filterObj="MSnIDFilter")
The filterObj argument is a "character" or converted to a "character" text string that is evaluated to a "logical" for each entry of the MS/MS results table. Return value is a filtered MSnID object with entries that pass the applied filter. See apply_filter

evaluate_filter

evaluate_filter(object, filter, level = c("PSM","peptide", "accession")
Returns a list with fdr and n elements. Argument filter is either "character" or "MSnIDFilter" object. Argument level can take one of the values c("PSM","peptide","accession") and controls the level filter is evaluated. See evaluate_filter

id_quality

signature(object="MSnID", ...)
Other optional ... arguments are filter is an "MSnIDFilter" instance and level. The level values are one of "PSM", "peptide", "accession". The method returns FDR for given level depending of type of identifications. See id_quality

as(,"MSnSet")

signature(x = "MSnID"): Coerce object from MSnID to MSnSet.

names

signature(x="MSnID")
Returns the column names in the MS/MS results table.

object$name, object$name<-value

Access and set name column in MS/MS search results table.

object[[i]], object[[i]]<-value

Access and set column i (character or numeric index) in MS/MS search results table.

as(,"MSnSet")

signature(from = "MSnID"): Coerce object from MSnID to MSnSet.

as(,"data.table")

signature(from = "MSnID"): Coerce object from MSnID to data.table.

Author(s)

Vladislav A Petyuk [e-mail]

See Also

MSnSet, mzID.

Examples

## Not run: 
msnidObj <- MSnID(".")
mzids <- system.file("extdata","c_elegans.mzid.gz",package="MSnID")
msnidObj <- read_mzIDs(msnidObj, mzids)
# clean up the cache directory
unlink(".Rcache", recursive=TRUE)

## End(Not run)

MSnID documentation built on Nov. 8, 2020, 8:03 p.m.