rownames: rownames

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

Description

Retrieve row names from LINCS gctx datafile

Usage

rownames(x, do.NULL = TRUE, prefix = "row")

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

Arguments

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

Value

Names of rows 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 rownames is desired, subset the slinky object itself, not the rownames, to avoid loading the entire set of rownames from the the gctx file. That is, names <- rownames(x[,1:50]) will be faster than names <- rownames(x)[1:50]. The do.NULL and prefix arguments from base::rownames do not apply here (as the slinky object will always have row 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'))
rownames(sl[1:5,])

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