Filter-classes: Filters supported by CompDb and IonDb

In EuracBiomedicalResearch/CompoundDb: Creating and Using (Chemical) Compound Annotation Databases

Filters supported by CompDb and IonDb

Description

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.

Author(s)

Johannes Rainer

See Also

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

Examples

## Create a filter for the compound id
cf <- CompoundIdFilter("comp_a")
cf

## Create a filter using a formula expression
AnnotationFilter(~ compound_id == "comp_b")

## Combine filters
AnnotationFilterList(CompoundIdFilter("a"), NameFilter("b"))

## Using a formula expression
AnnotationFilter(~ compound_id == "a" | name != "b")

EuracBiomedicalResearch/CompoundDb documentation built on Oct. 1, 2024, 2:16 p.m.