Loading Gene Expression Deconvolution Data

Description

gedData loads entries from the CellMix dataset registry.

gedDataInfo prints information about the registered gene expression datasets or returns -- invisibly -- the complete dataset registry, as a registry object.

Usage

gedData(key, error = TRUE, all = FALSE, exact = FALSE, with = NULL, ...)

gedDataInfo(show = TRUE)

Arguments

with
character vector, only used when key is missing, that specifies some filtering criterium. It allows to only list datasets that contain specific data, which may help choosing a suitable dataset when developping/testing deconvolution methods:
  1. 'prop'cell proportions for each samples.
  2. 'sig'cell-specific sigantures.
  3. 'all'both proportions and cell-specific signatures.
  4. 'mixed'mixed samples.
  5. 'pure'pure samples.
Any combination of these is allowed, e.g. c('prop', 'pure') to list datasets that contain proportions and pure samples.
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 '.'.
exact
logical that indicates if one should use exact matching or partial matching to match the provided access key against all registered keys.
...
extra arguments used internally, not to be used by the end user.

Value

a GEDdata_entry object or NULL (see argument error)

Examples


# retrieve a dataset entry
gedData('GSE20300')
##                key GSE20300
##            aliases 
##                url 
##        description Whole blood from stable and acute rejection
##                    pediatric kidney transplant
##               cite Shen-Orr2010
##         annotation hgu133plus2.db
##                dim 54675, 24, 5
##              basis NA
##               coef <<function>>
##               pure NA
##                env <environment>
##              pdata <<function>>
##              fdata NA
##             filter NA
## REGISTERINGpackage CellMix

# error if the entry does not exists
try( gedData('GSE1234') )
# unless error=FALSE
gedData('GSE1234', error=FALSE)
## NULL

# list datasets that contain cell proportions
gedData(with='prop')
## [1] "GSE29832"   "GSE19830"   "GSE20300"   "GSE5350"    "GSE11058"  
## [6] "GSE33076"   "GSE3649"    "E-TABM-633" "GSE24759"
# or pure samples
gedData(with='sig')
## [1] "GSE29832"   "GSE19830"   "GSE5350"    "GSE11057"   "GSE11058"  
## [6] "GSE33076"   "E-TABM-633" "GSE24759"
# or both
gedData(with=c('prop', 'sig'))
## [1] "GSE29832"   "GSE19830"   "GSE5350"    "GSE11058"   "GSE33076"  
## [6] "E-TABM-633" "GSE24759"
# or mixed samples
gedData(with='mixed')
## [1] "GSE29832" "GSE24223" "GSE19830" "GSE20300" "GSE5350"  "GSE11057"
## [7] "GSE11058" "GSE33076" "GSE3649"
# show algorithms and properties
gedDataInfo()
## An object of class 'registry' with 13 entries.
##                                                                                                                Description
## GSE29832                                             Pure/mixed blood and breast to test deconvolution of clinical samples
## GSE24223                                          Deconvoluting Early Post-Transplant Immunity Using Purified Cell Subsets
## GSE19830                                          Pure/mixed brain, liver and lung to test statistical deconvolution [Rat]
## GSE20300                                           Whole blood from stable and acute rejection pediatric kidney transplant
## GSE5350                                             MicroArray Quality Control (MAQC) Project: Affymetrix HG-U133 Plus 2.0
## GSE11057                                                     Memory T Cell Subsets: Central memory, Effector memory, Naive
## GSE11058                                                              Immune Cell Line Mixtures: Jurkat, IM-9, Raji, THP-1
## GSE22886_A                                                       IRIS: Resting and activated human immune cells [HG-U133A]
## GSE22886_B                                                       IRIS: Resting and activated human immune cells [HG-U133B]
## GSE33076                                Linearity of amplification between gene expression values and mRNA in retina cells
## GSE3649                                             Individuality and variation in gene expression patterns in human blood
## E-TABM-633                                      The HaemAtlas: Transcription profiling of differentiated human blood cells
## GSE24759   Differentiation Map: Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis
##            Features Samples Types Mixed  Pure Basis  Coef
## GSE29832      54675      15     2  TRUE  TRUE  TRUE  TRUE
## GSE24223      54675     179     5  TRUE  TRUE FALSE FALSE
## GSE19830      31099      42     3  TRUE  TRUE  TRUE  TRUE
## GSE20300      54675      24     5  TRUE FALSE FALSE  TRUE
## GSE5350       54675     120     2  TRUE  TRUE  TRUE  TRUE
## GSE11057      54675      17     3  TRUE  TRUE  TRUE FALSE
## GSE11058      54675      24     4  TRUE  TRUE  TRUE  TRUE
## GSE22886_A    22283     114    11 FALSE  TRUE FALSE FALSE
## GSE22886_B    22645     114    11 FALSE  TRUE FALSE FALSE
## GSE33076      22347      24     2  TRUE  TRUE  TRUE  TRUE
## GSE3649       36794      70     5  TRUE FALSE FALSE  TRUE
## E-TABM-633    46693      50     8 FALSE  TRUE  TRUE  TRUE
## GSE24759      22944     211    38 FALSE  TRUE  TRUE  TRUE
##                       Annotation       Reference
## GSE29832          hgu133plus2.db        Gong2011
## GSE24223          hgu133plus2.db   Grigoryev2010
## GSE19830              rat2302.db    Shen-Orr2010
## GSE20300          hgu133plus2.db    Shen-Orr2010
## GSE5350           hgu133plus2.db         Shi2006
## GSE11057          hgu133plus2.db       Abbas2009
## GSE11058          hgu133plus2.db       Abbas2009
## GSE22886_A            hgu133a.db       Abbas2005
## GSE22886_B            hgu133b.db       Abbas2005
## GSE33076   mogene10stprobeset.db     Siegert2012
## GSE3649                              Whitney2003
## E-TABM-633    illuminaHumanv2.db     Watkins2009
## GSE24759            hthgu133a.db Novershtern2011
class(gedDataInfo(FALSE))
## [1] "GEDdata_registry"      "data_package_registry" "package_registry"     
## [4] "registry"