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A thin wrapper around Rlabkey to access the ImmuneSpace Data & Tools Portal 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.
interactive_netrc()function in R:
If you’re familiar with the command-line interface, see the introductory vignette.
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:
which will print names of available datasets and gene expression matrices.
Gene expression matrices or datasets can be retreived by:
LAIV2008 <- con$getGEMatrix("SDY269_PBMC_LAIV_Geo") elisa <- con$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.
For more advanced examples and detailed documentation, see the package vignettes and the reports available on ImmuneSpace.
If you’d like to report bugs/issues/feature requests or contribute to the package, please see the contributing guidelines and join our Slack workspace.