inst/doc/ExpressionAtlas.R

In ExpressionAtlas: Download datasets from EMBL-EBI Expression Atlas

## -----------------------------------------------------------------------------
suppressMessages( library( ExpressionAtlas ) )

## ----eval=FALSE---------------------------------------------------------------
#  atlasRes <- searchAtlasExperiments( properties = "salt", species = "rice" )
#  # Searching for Expression Atlas experiments matching your query ...
#  # Query successful.
#  # Found 3 experiments matching your query.

## ---- echo=FALSE--------------------------------------------------------------
data( "atlasRes" )

## -----------------------------------------------------------------------------
atlasRes

## ----eval=FALSE---------------------------------------------------------------
#  allExps <- getAtlasData( atlasRes$Accession )
#  # Downloading Expression Atlas experiment summary from:
#  #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-GEOD-11175/E-GEOD-11175-atlasExperimentSummary.Rdata
#  # Successfully downloaded experiment summary object for E-GEOD-11175
#  # Downloading Expression Atlas experiment summary from:
#  #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1625/E-MTAB-1625-atlasExperimentSummary.Rdata
#  # Successfully downloaded experiment summary object for E-MTAB-1625
#  # Downloading Expression Atlas experiment summary from:
#  #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1624/E-MTAB-1624-atlasExperimentSummary.Rdata
#  # Successfully downloaded experiment summary object for E-MTAB-1624

## ---- echo=FALSE--------------------------------------------------------------
data( "allExps" )

## -----------------------------------------------------------------------------
allExps

## ----eval=FALSE---------------------------------------------------------------
#  rnaseqExps <- getAtlasData(
#      atlasRes$Accession[
#          grep(
#              "rna-seq",
#              atlasRes$Type,
#              ignore.case = TRUE
#          )
#      ]
#  )
#  # Downloading Expression Atlas experiment summary from:
#  #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1625/E-MTAB-1625-atlasExperimentSummary.Rdata
#  # Successfully downloaded experiment summary object for E-MTAB-1625

## ---- echo=FALSE--------------------------------------------------------------
data( "rnaseqExps" )

## -----------------------------------------------------------------------------
rnaseqExps

## -----------------------------------------------------------------------------
mtab1624 <- allExps[[ "E-MTAB-1624" ]]
mtab1625 <- allExps[[ "E-MTAB-1625" ]]

## -----------------------------------------------------------------------------
sumexp <- mtab1625$rnaseq
sumexp

## -----------------------------------------------------------------------------
head( assays( sumexp )$counts )

## -----------------------------------------------------------------------------
colData( sumexp )

## -----------------------------------------------------------------------------
metadata( sumexp )

## -----------------------------------------------------------------------------
names( mtab1624 )
affy126data <- mtab1624[[ "A-AFFY-126" ]]
affy126data

## -----------------------------------------------------------------------------
head( exprs( affy126data ) )

## -----------------------------------------------------------------------------
pData( affy126data )

## -----------------------------------------------------------------------------
preproc( experimentData( affy126data ) )

## ----eval=FALSE---------------------------------------------------------------
#  mtab3007 <- getAtlasExperiment( "E-MTAB-3007" )
#  # Downloading Expression Atlas experiment summary from:
#  #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-3007/E-MTAB-3007-atlasExperimentSummary.Rdata
#  # Successfully downloaded experiment summary object for E-MTAB-3007