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.
pRolocmarkers(species)The species of interest.
Prints a description of the available marker lists if
species is missing or a named character with organelle
markers.
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.
addMarkers to add markers to an
MSnSet and markers for more information about
marker encoding.
pRolocmarkers()
#> 7 marker lists available:
#> Arabidopsis thaliana [atha]:
#> Ids: TAIR, 543 markers
#> Drosophila melanogaster [dmel]:
#> Ids: Uniprot, 179 markers
#> Gallus gallus [ggal]:
#> Ids: IPI, 102 markers
#> Homo sapiens [hsap]:
#> Ids: Uniprot, 872 markers
#> Mus musculus [mmus]:
#> Ids: Uniprot, 937 markers
#> Saccharomyces cerevisiae [scer_sgd]:
#> Ids: SGD, 259 markers
#> Saccharomyces cerevisiae [scer_uniprot]:
#> Ids: Uniprot Accession, 259 markers
table(pRolocmarkers("atha"))
#>
#> ENV ER ER lumen ER membrane Golgi
#> 46 30 9 42 27
#> Mitochondrion PM Plastid Ribosome STR
#> 103 60 48 8 83
#> TGN THY Vacuole
#> 13 56 18
table(pRolocmarkers("hsap"))
#>
#> 40S Ribosome 60S Ribosome Cytosol
#> 33 46 77
#> Endoplasmic Reticulum Golgi Apparatus Lysosome
#> 92 34 42
#> Mitochondria Nucleus PEROXISOME
#> 134 116 27
#> Proteasome actin cytoskeleton plasma mem
#> 36 45 190