README.md

In ddiez/immgen.db: A Package with Data from the Immgen Project

immgen.db

This package contains data compiled from the Immunological Genome Project (ImmGen). Currently it contains expression data and the ontogeny.

Installation

Because the expression dataset is larger than 100 Mb it is stored in a LFS repository. Therefore you need to install git-lfs in order to properly clone this repository. Follow the instructions here. Once you have git-lfs then you can obtain immgen.db from github:

devtools::install_github("ddiez/immgen.db")

Usage

library(immgen.db)
immgen # ExpressionSet object with 22,135 features and 678 samples.

## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 22135 features, 678 samples 
##   element names: exprs 
## protocolData
##   sampleNames: GSM399362 GSM399363 ... GSM920647 (678 total)
##   varLabels: ScanDate
##   varMetadata: labelDescription
## phenoData
##   sampleNames: GSM399362 GSM399363 ... GSM920647 (678 total)
##   varLabels: FileName CellType
##   varMetadata: labelDescription
## featureData
##   featureNames: 100009600_at 100009609_at ... 99982_at (22135
##     total)
##   fvarLabels: ENTREZID SYMBOL GENENAME
##   fvarMetadata: labelDescription
## experimentData: use 'experimentData(object)'
## Annotation: mogene10stmmentrezg

ddiez/immgen.db documentation built on May 15, 2019, 1:51 a.m.