isobar (version 1.18.0)

subsetIBSpectra: Subset IBSpectra objects

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

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")