coerce {slinky}R Documentation

as("Slinky", "SummarizedExperiment")

Description

Create SummarizedExperiment object from Slinky object. Data will be loaded from the GCTX file, combined with metadata from the info file, and wrapped in a SummarizedExperiment object. Note that this may take a long time for the entire data set from the L1000 project. For most use cases, a subset will be desired (e.g. as(sl[1:987,1:50], SummarizedExperiment). See the loadL1K method for a more flexible way to create a SummarizedExperiment object based on various query parameters.

See Also

loadL1K

Examples


# for build/demo only.  You MUST use your own key when using the slinky
# package.
user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
                          as='parsed')$user_key
sl <- Slinky(user_key,
                 system.file('extdata', 'demo.gctx',
                      package='slinky'),
                 system.file('extdata', 'demo_inst_info.txt',
                     package = 'slinky'))
sumex <- as(sl[, 1:20], "SummarizedExperiment")


[Package slinky version 1.8.0 Index]