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<!-- is generated from README.Rmd. Please edit that file --> # ImmuneSpaceR <img src="man/figures/logo.png" align="right" /> [![Build Status](]( [![codecov](]( [![bioc](]( [![bioc](]( A thin wrapper around Rlabkey to access the [ImmuneSpace](%22 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. ## Installation Install from [Bioconductor]( ``` r source("") biocLite("ImmuneSpaceR") ``` Or install the latest development version via [`devtools`]( ``` r devtools::install_github("RGLab/ImmuneSpaceR") ``` The database is accessed with the user’s credentials. A `.netrc` file storing login and password information is required. Create netrc file in the computer running R: - On a **UNIX** system, this file should be named `.netrc` - On **Windows**, it sould be named `_netrc` - The file should be located in the user’s **home** directory - To determine home directory, run `Sys.getenv("HOME")` in R - The permissions on this file should be unreadable for everybody except the owner The following three lines must be included in the `.netrc` or `_netrc` file either separated by white space (spaces, tabs, or newlines) or commas. machine login password superSecretPassword Multiple such blocks can exist in one file. Please ensure that the machine name in the netrc file contains the “www” prefix as that is how the package connects to immunespace by default. A mismatch will lead to connection failures. See [the official documentation]( from LabKey and the introductory vignette for an ImmuneSpace specific setup. ## Usage ### 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. For example: ``` r library(ImmuneSpaceR) study <- CreateConnection("SDY269") ``` will create an instance of SDY269. ### List datasets Datasets can be listed by: ``` r study$listDatasets() #> datasets #> demographics #> elispot #> hai #> fcs_analyzed_result #> cohort_membership #> pcr #> elisa #> gene_expression_files #> fcs_sample_files #> Expression Matrices #> SDY269_PBMC_TIV_Geo #> SDY269_PBMC_LAIV_Geo ``` which will print names of available datasets and gene expression matrices. ### Retrieve datasets Gene expression matrices or datasets can be retreived by: ``` r LAIV2008 <- study$getGEMatrix("SDY269_PBMC_LAIV_Geo") #> Downloading matrix.. #> Constructing ExpressionSet elisa <- study$getDataset("elisa") ``` The study object *caches* data, so once it is retrieved, the next time you access it, it will use the local cached copy. The package uses a [R6]( class system to represent the connection to a study and get around some of R’s copy-on-change behaviour. ### Visualize The `plot` method uses [`ggplot2`]( functions to generate visualizations of datasets, leveraging the standardized dataset tables. ``` r study$plot("hai") ``` <img src="man/figures/README-plot-1.png" width="100%" /> ## Examples & Documentation For more advanced examples and detailed documentation, see the package vignettes and the reports available on [ImmuneSpace]( ## Contributing 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](