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

Description

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

Arguments

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.

Examples

Run this code

## 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)