pRolocmarkers: Organelle markers

In pRoloc: A unifying bioinformatics framework for spatial proteomics

Description

This function retrieves a list of organelle markers or, if no species is provided, prints a description of available marker sets. The markers can be added to and MSnSet using the addMarkers function.

Usage

pRolocmarkers(species)

Arguments

species

The species of interest.

Details

The markers have been contributed by various members of the Cambridge Centre for Proteomics, in particular Dr Dan Nightingale for yeast, Dr Andy Christoforou and Dr Claire Mulvey for human, Dr Arnoud Groen for Arabodopsis and Dr Claire Mulvey for mouse. In addition, original (curated) markers from the pRolocdata datasets have been extracted (see pRolocdata for details and references). Curation involved verification of publicly available subcellular localisation annotation based on the curators knowledge of the organelles/proteins considered and tracing the original statement in the literature.

These markers are provided as a starting point to generate reliable sets of organelle markers but still need to be verified against any new data in the light of the quantitative data and the study conditions.

Value

Prints a description of the available marker lists if species is missing or a named character with organelle markers.

Author(s)

Laurent Gatto

See Also

addMarkers to add markers to an MSnSet and markers for more information about marker encoding.

Examples

pRolocmarkers()
table(pRolocmarkers("atha"))
table(pRolocmarkers("hsap"))

pRoloc documentation built on Nov. 8, 2020, 6:26 p.m.