A thin wrapper around Rlabkey to access the ImmuneSpace database from R.
This package simplifies access to the HIPC ImmuneSpace database for R programmers. It takes advantage of the standardization of the database to hide all the
Rlabkey specific code away from the user. The study-specific datasets can be accessed via an object-oriented paradigm.
Install from Bioconductor:
Or install the latest development version via
The ImmuneSpace Portal can be accessed via
ImmuneSpaceR with the user's credentials. A
.netrc file storing login and password information is required.
- Create a netrc file with your ImmuneSpace credetntials using
interactive_netrc()function in R:
If you're familiar with the command-line interface, see the introductory vignette.
Create a connection
The general idea is that the user creates an instance of an
ImmuneSpaceConnection class. The instance configures itself to connect to a specific study, and datasets and gene expression matrices can be retrieved by name.
library(ImmuneSpaceR) con <- CreateConnection("SDY269")
will create an instance of SDY269.
Datasets can be listed by:
con$listDatasets() #> datasets #> gene_expression_files #> fcs_sample_files #> demographics #> elispot #> hai #> elisa #> pcr #> cohort_membership #> fcs_analyzed_result #> Expression Matrices #> SDY269_PBMC_TIV_Geo #> SDY269_PBMC_LAIV_Geo
which will print names of available datasets and gene expression matrices.
Gene expression matrices or datasets can be retreived by:
LAIV2008 <- con$getGEMatrix("SDY269_PBMC_LAIV_Geo") #> Downloading matrix.. #> Constructing ExpressionSet elisa <- con$getDataset("elisa")
The connection object caches data, so once it is retrieved, the next time you access it, it will use the local cached copy. The package uses a R6 class system to represent the connection to a study and get around some of R's copy-on-change behaviour.
plot method uses
ggplot2 functions to generate visualizations of datasets, leveraging the standardized dataset tables.