Filter-classes: Filters supported by CompDb

In michaelwitting/CompoundDb: Creating and using (Chemical) Compound Annotation Databases

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.

• CompoundNameFilter: 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).

Usage

CompoundIdFilter(value, condition = "==")

CompoundNameFilter(value, condition = "==")

MsmsMzRangeMinFilter(value, condition = ">=")

MsmsMzRangeMaxFilter(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().

Author(s)

Johannes Rainer

See Also

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

Examples

library(CompoundDb)

## 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"), CompoundNameFilter("b"))

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

michaelwitting/CompoundDb documentation built on April 29, 2020, 8:42 p.m.