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Hughes2009: Circadian Liver Transcriptome

The Hughes2009 package provides processed liver transcriptome data from the Hughes et al. (2009) study on circadian rhythms. It contains normalized expression data and gene-level summaries, designed for testing circadian analysis workflows and co-expression network construction.

Installation

You can install the development version of Hughes2009 from GitHub:

install.packages("pak")
pak::pak("altintasali/Hughes2009")

Quick Start

This package provides an ExpressionSet object containing mouse liver microarray data across a 48-hour period.

# Load the dataset
data(eset)

# Peek at the data
show(eset)
## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 45101 features, 48 samples 
##   element names: exprs 
## protocolData
##   sampleNames: GSM301348.CEL.gz GSM301349.CEL.gz ... GSM301395.CEL.gz
##     (48 total)
##   varLabels: ScanDate
##   varMetadata: labelDescription
## phenoData
##   sampleNames: GSM301348 GSM301349 ... GSM301395 (48 total)
##   varLabels: title geo_accession ... relation.1 (33 total)
##   varMetadata: labelDescription
## featureData
##   featureNames: 1415670_at 1415671_at ... AFFX-r2-P1-cre-5_at (45101
##     total)
##   fvarLabels: PROBEID SYMBOL GENENAME MAS5_CALL
##   fvarMetadata: labelDescription
## experimentData: use 'experimentData(object)'
## Annotation: mouse4302
# Extract expression matrix
expression_matrix <- exprs(eset)

# Print first 6 rows and columns
print(expression_matrix[1:6, 1:6])
##              GSM301348.CEL.gz GSM301349.CEL.gz GSM301350.CEL.gz
## 1415670_at          10.047478        10.144396        10.032522
## 1415671_at          10.742481        10.572902        10.678695
## 1415672_at          11.134648        11.113839        11.060911
## 1415673_at           8.123238         8.375692         8.467279
## 1415674_a_at         8.814808         8.788226         8.699853
## 1415675_at           7.563833         7.303640         7.322527
##              GSM301351.CEL.gz GSM301352.CEL.gz GSM301353.CEL.gz
## 1415670_at           9.804604         9.990287         9.682311
## 1415671_at          10.648379        10.714002        10.591531
## 1415672_at          11.280906        11.074163        11.186339
## 1415673_at           8.129796         8.236522         8.042468
## 1415674_a_at         8.768019         8.587714         8.366756
## 1415675_at           7.430643         7.668505         7.474612
# Extract metadata
meta <- pData(eset)

# Print first 6 rows and columns
print(meta[1:6, 1:6])
##                                  title geo_accession                status
## GSM301348 Circadian time 18 Liver_CT18     GSM301348 Public on Oct 03 2008
## GSM301349 Circadian time 19 Liver_CT19     GSM301349 Public on Oct 03 2008
## GSM301350 Circadian time 20 Liver_CT20     GSM301350 Public on Oct 03 2008
## GSM301351 Circadian time 21 Liver_CT21     GSM301351 Public on Oct 03 2008
## GSM301352 Circadian time 22 Liver_CT22     GSM301352 Public on Oct 03 2008
## GSM301353 Circadian time 23 Liver_CT23     GSM301353 Public on Oct 03 2008
##           submission_date last_update_date type
## GSM301348     Jun 27 2008      Aug 28 2018  RNA
## GSM301349     Jun 27 2008      Aug 28 2018  RNA
## GSM301350     Jun 27 2008      Aug 28 2018  RNA
## GSM301351     Jun 27 2008      Aug 28 2018  RNA
## GSM301352     Jun 27 2008      Aug 28 2018  RNA
## GSM301353     Jun 27 2008      Aug 28 2018  RNA

Vignettes

For more detailed overview, please checkout the vignette:

Full Documentation

Read the full documentation and tutorials online