Description Objects from the Class Slots Methods Author(s) See Also Examples
The MSnID
is a convenience class for manipulating
the MS/MS search results.
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
.
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.
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
signature(x = "MSnID")
:
Returns the dimensions of
the table with MS/MS identification data.
signature(object = "MSnID")
:
Returns unique peptide list. See peptides
signature(object = "MSnID")
:
Returns unique accessions (typically proteins) list.
See accessions
signature(object = "MSnID")
:
Returns unique proteins list.
See proteins
Checks the agreement of peptide termini
with enzymes cleavage specificity. The return value is
theMSnID
object with extra variable numIrregCleavages
.
See assess_termini
Checks if the peptide sequence contains the
sites that were not cleaved by the enzyme.
For details see assess_missed_cleavages
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
Recalibrates, that is removes systematic
error from experimentalMassToCharge
measurements.
See recalibrate
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
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(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
signature(x = "MSnID")
:
Coerce object from MSnID
to MSnSet
.
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.
signature(from = "MSnID")
:
Coerce object from MSnID
to MSnSet
.
signature(from = "MSnID")
:
Coerce object from MSnID
to data.table
.
Vladislav A Petyuk vladislav.petyuk@pnnl.gov
1 2 3 4 5 6 7 8 | ## 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)
|
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