R/functions-addIdentificationData.R
filterIdentificationDataFrame.Rd
A function to filter out PSMs matching to the decoy database, of rank greater than one and matching non-proteotypic peptides.
filterIdentificationDataFrame(
x,
decoy = "isDecoy",
rank = "rank",
accession = "DatabaseAccess",
spectrumID = "spectrumID",
verbose = isMSnbaseVerbose()
)
A data.frame
containing PSMs.
The column name defining whether entries match the
decoy database. Default is "isDecoy"
. The column should be a
logical
and only PSMs holding a FALSE
are
retained. Ignored is set to NULL
.
The column name holding the rank of the PSM. Default
is "rank"
. This column should be a numeric
and only PSMs
having rank equal to 1 are retained. Ignored is set to NULL
.
The column name holding the protein (groups)
accession. Default is "DatabaseAccess"
. Ignored is set to
NULL
.
The name of the spectrum identifier
column. Default is spectrumID
.
A logical
verbosity flag. Default is to take
isMSnbaseVerbose()
.
A new data.frame
with filtered out peptides and with the
same columns as the input x
.
The PSMs should be stored in a data.frame
such as those produced
by readMzIdData()
. Note that this function should be called
before calling the reduce method on a
PSM data.frame
.