subsetIBSpectra: Subset IBSpectra objects

In fbreitwieser/isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

Returns an IBSpectra object which is a subset of the input, excluding or exclusively containing the peptides or proteins supplied.

Usage

subsetIBSpectra(x, protein = NULL, peptide = NULL,
                direction = "exclude",
                specificity = c(REPORTERSPECIFIC, GROUPSPECIFIC, UNSPECIFIC), ...)

Arguments

x	IBSpectra object.
protein	Protein group identifiers. Use protein.g to get protein group identifiers from protein database ACs.
peptide	Peptide sequences.
direction	either 'include' or 'exclude'.
specificity	When 'protein' is supplied: Which peptides should be selected? See specificities.
...	Further arguments passed to spectrumSel

Author(s)

Florian P Breitwieser

See Also

protein.g, spectrumSel, specificities

Examples

data(ibspiked_set1)

# get Keratin proteins
keratin.proteins <- protein.g(proteinGroup(ibspiked_set1),"Keratin")

# exclude Keratin proteins
subsetIBSpectra(ibspiked_set1,protein=keratin.proteins,direction="exclude")

fbreitwieser/isobar documentation built on May 16, 2019, 12:01 p.m.