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.
gedData(key, error = TRUE, all = FALSE, exact = FALSE, with = NULL, ...) gedDataInfo(show = TRUE)
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: 'prop'
cell proportions for each samples.
'sig'
cell-specific sigantures.
'all'
both proportions and cell-specific
signatures. 'mixed'
mixed samples.
'pure'
pure samples. c('prop',
'pure')
to list datasets that contain proportions and
pure samples.FALSE
) or only returned
invisibly (FALSE
).FALSE
then function
returns NULL
if the key is not found or NA
in case of multiple matches.key
is
missing and indicates if all registered keys should be
returned, including the internal one -- whose key starts
with a '.'.a GEDdata_entry
object or NULL
(see
argument error
)
# 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"