colnames {slinky} | R Documentation |
Retrieve column names from LINCS gctx datafile
colnames(x, do.NULL = TRUE, prefix = "col") ## S4 method for signature 'Slinky' colnames(x)
x |
a Slinky Object |
do.NULL |
Ignored (see |
prefix |
Ignored (see |
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.
# 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])