collapseHypothesis: Collapse redundant hypotheses

In CCprofiler/CCprofiler: Complex feature detection using SEC protein chromatograms.

Description

Remove redundancy in existing complex hypotheses

Usage

collapseHypothesis(hypothesis, redundancy_cutoff = 1)

Arguments

hypothesis	data.table with complex hypotheses Must have the following columns: complex_id: character strings, a unique id for every complex protein_id: character strings, the protein id, e.g. Uniprot id Additionaly a complex_name column is allowed.
redundancy_cutoff	Numeric, maximum overlap distance between two hypotheses 0 = identical 1 = subset between 1 and 2 = some shared subunits 2 = no shared subunits Defaults to 1.

Value

data.table in the format of complex hypotheses Has the following columns:

• complex_id: character strings, a unique id for every complex

• complex_name: character strings, Name of the complex

• protein_id: character strings, the protein id, e.g. Uniprot id

Examples

## load example data
complexHypotheses <- exampleComplexHypotheses
## Collapse redundancies
complexHypothesesCollapsed <- collapseHypothesis(complexHypotheses)

CCprofiler/CCprofiler documentation built on May 19, 2021, 7:40 p.m.