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Filters supported by CompDb and IonDb

Source: R/AnnotationFilters.R
Filter-classes.Rd

A variety of different filters can be applied to the CompDb object to retrieve only subsets of the data. These filters extend the AnnotationFilter::AnnotationFilter class and support the filtering concepts introduced by Bioconductor's AnnotationFilter package.

The supported filters are:

  • CompoundIdFilter: filter based on the compound ID.

  • FormulaFilter: filter based on the compound's formula.

  • InchiFilter: filter based on the compound's InChI.

  • InchikeyFilter: filter based on the compound's InChI key.

  • ExactmassFilter: filter based on the compound's (exact) mass.

  • NameFilter: filter based on the compound name.

  • MsmsMzRangeMinFilter: retrieve entries based on the smallest m/z of all peaks of their MS/MS spectra. Requires that MS/MS spectra data are present (i.e. hasMsMsSpectra(cmp_db) returns TRUE).

  • MsmsMzRangeMaxFilter: retrieve entries based on the largest m/z of all peaks of their MS/MS spectra. Requires that MS/MS spectra data are present (i.e. hasMsMsSpectra(cmp_db) returns TRUE).

  • SpectrumIdFilter: retrieve entries associated with the provided IDs of MS/MS spectra.

In addition to the filters listed above, the following ones are supported by a IonDb (but not by a CompDb):

  • IonIdFilter: filter based on the ion ID.

  • IonAdductFilter: filter based on the adduct.

  • IonMzFilter: filter based on the mz of the ion.

  • IonRtFilter: filter based on the rt of the ion.

Usage

CompoundIdFilter(value, condition = "==")

SpectrumIdFilter(value, condition = "==")

NameFilter(value, condition = "==")

MsmsMzRangeMinFilter(value, condition = ">=")

MsmsMzRangeMaxFilter(value, condition = "<=")

ExactmassFilter(value, condition = "==")

FormulaFilter(value, condition = "==")

InchiFilter(value, condition = "==")

InchikeyFilter(value, condition = "==")

IonIdFilter(value, condition = "==")

IonAdductFilter(value, condition = "==")

IonMzFilter(value, condition = "==")

IonRtFilter(value, condition = "==")

Arguments

value

The value for the filter. For details see AnnotationFilter::AnnotationFilter().

condition

The condition for the filter. For details see AnnotationFilter::AnnotationFilter().

Value

Constructor functions return an instance of the respective class.

See also

supportedFilters() for the method to list all supported filters for a CompDb (or a IonDb) object.

Author

Johannes Rainer

Examples

## Create a filter for the compound id
cf <- CompoundIdFilter("comp_a")
cf
#> class: CompoundIdFilter 
#> condition: == 
#> value: comp_a 

## Create a filter using a formula expression
AnnotationFilter(~ compound_id == "comp_b")
#> class: CompoundIdFilter 
#> condition: == 
#> value: comp_b 

## Combine filters
AnnotationFilterList(CompoundIdFilter("a"), NameFilter("b"))
#> AnnotationFilterList of length 2 
#> compound_id == 'a' & name == 'b'

## Using a formula expression
AnnotationFilter(~ compound_id == "a" | name != "b")
#> AnnotationFilterList of length 2 
#> compound_id == 'a' | name != 'b'