A thin wrapper around Rlabkey to access the ImmuneSpace database from R
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README.md

ImmuneSpaceR

Build Status codecov bioc bioc

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.

Installation

Install from Bioconductor:

source("https://bioconductor.org/biocLite.R")
biocLite("ImmuneSpaceR")

Or install the latest development version via devtools:

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 www.immunespace.org
login myUser@mySite.com
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:

library(ImmuneSpaceR)
study <- CreateConnection("SDY269")

will create an instance of SDY269.

List datasets

Datasets can be listed by:

study$listDatasets()
#> datasets
#>  demographics
#>  elisa
#>  gene_expression_files
#>  hai
#>  cohort_membership
#>  pcr
#>  fcs_sample_files
#>  fcs_analyzed_result
#>  elispot
#> Expression Matrices
#>  LAIV_2008
#>  TIV_2008

which will print names of available datasets and gene expression matrices.

Retrieve datasets

Gene expression matrices or datasets can be retreived by:

LAIV2008 <- study$getGEMatrix("LAIV_2008")
#> Downloading matrix..
#> Constructing ExpressionSet
elisa <- study$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.

study$plot("hai")

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.