readGCTX: readGCTX

In VanAndelInstitute/slinky: Putting the fun in LINCS L1000 data analysis

Description

Read portions of data matrix from LINCS gctx datafile

Usage

readGCTX(x)

## S4 method for signature 'Slinky'
readGCTX(x)

Arguments

x	a Slinky Object

Value

Matrix of expression data with rownames and colnames appropriately set. If a subset of the data is desired, subset the slinky object itself, not the resulting data matrix. That is, data <- readGCTX(x[1:50,1:500]) will be MUCH faster than ndata <- readGCTX(x)[1:50, 1:500].

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'))
data <- readGCTX(sl[1:20,1:5])

VanAndelInstitute/slinky documentation built on Aug. 20, 2021, 1:05 p.m.