CellMix 1.6

Loading Marker Lists from Registry

Description

Loading Marker Lists from Registry

cellMarkersInfo prints information about the registered marker gene lists or return the complete marker list registry, as a registry object.

Usage

cellMarkers(key, error = TRUE, verbose = FALSE, all = FALSE, ...)

cellMarkersInfo(show = TRUE)

Arguments

verbose
logical that toggles verbose messages.
...
arguments passed to the marker list's loading function. In particular argument reload=TRUE can be used to clear the cache and force reloading/recomputing the marker list from its primary data file.
show
logical that indicates if the registry object should be printed (FALSE) or only returned invisibly (FALSE).
key
algorithm access key, as a single character string. If missing the function returns the list of registered keys, as a character vector.
error
a logical that indicates whether an error should be thrown if the key is not found in the registry or match multiple lists. If FALSE then function returns NULL if the key is not found or NA in case of multiple matches.
all
logical that is only used when key is missing and indicates if all registered keys should be returned, including the internal one -- whose key starts with a '.'.

Value

a GEDmarkers_entry object or NULL (see argument error)

Examples


# show marker lists and properties
cellMarkersInfo()

##                                                                                                        Description
## IRIS                            Immune Response In Silico: B, T, NK and dendritic cells, monocytes and neutrophils
## Abbas                                             Optimised set of immune genes for deconvolution of blood samples
## TDDB_HS                  TissueDistributionDB: UniGene EST distribution profiles using Tissue Ontology from BRENDA
## TDDB_RN                  TissueDistributionDB: UniGene EST distribution profiles using Tissue Ontology from BRENDA
## Palmer                                    Markers for B-cells, CD4+ and CD8+ T-cells, lymphocytes and granulocytes
## HaemAtlas HaemAtlas markers for CD4+ and CD8+ T-cells, lymphocytes, monocytes, B-cells, NK cells, and granulocytes
## TIGER                                                   TiGER database: based on UniGene EST distribution profiles
## VeryGene                                                 VeryGene database: based on two large microarray datasets
## .CDBlood                                                                                      CD markers for blood
## Grigoryev                                                               Cytometry antigen markers for immune cells
##           Organism Types Markers      idType             Annotation
## IRIS         Human     9    2270 .Affymetrix hgu133a.db, hgu133b.db
## Abbas        Human    12     122 .Affymetrix hgu133a.db, hgu133b.db
## TDDB_HS      Human    65   14732     UNIGENE           org.Hs.eg.db
## TDDB_RN        Rat    19    3915     UNIGENE           org.Rn.eg.db
## Palmer       Human     5     907      SYMBOL           org.Hs.eg.db
## HaemAtlas    Human     8    2069   .Illumina     illuminaHumanv2.db
## TIGER        Human    30    7743     UNIGENE           org.Hs.eg.db
## VeryGene     Human   127   10102    ENTREZID           org.Hs.eg.db
## .CDBlood     Human     4       5                       org.Hs.eg.db
## Grigoryev    Human    11     157 .Affymetrix         hgu133plus2.db
##               Reference
## IRIS          Abbas2005
## Abbas         Abbas2009
## TDDB_HS    Kogenaru2009
## TDDB_RN    Kogenaru2009
## Palmer       Palmer2006
## HaemAtlas   Watkins2009
## TIGER          Liu2008a
## VeryGene       Yang2011
## .CDBlood               
## Grigoryev Grigoryev2010

class(cellMarkersInfo(FALSE))

## [1] "GEDmarkers_registry"      "markers_package_registry"
## [3] "package_registry"         "registry"