colnames: colnames

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

Description

Retrieve column names from LINCS gctx datafile

Usage

colnames(x, do.NULL = TRUE, prefix = "col")

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

Arguments

x	a Slinky Object
do.NULL	Ignored (see ?base::colnames)
prefix	Ignored (see ?base::colnames)

Value

Names of columns from gctx file The gctx file is an HDF5 formatted file with several sections (groups) containing the column and row level metadata as well as the expression data itself. Note that for best performance, if a subset of colnames is desired, subset the slinky object itself, not the colnames, to avoid loading the entire set of colnames from the the gctx file. That is, names <- colnames(x[,1:50]) will be considerably faster than names <- colnames(x)[1:50]. The do.NULL and prefix arguments from base::colnames do not apply here (as the slinky object will always have column names), and will be silently ignored if provided.

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'))
colnames(sl[,1:5])

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