scOpen: Open a Single-cell GDS File

In zhengxwen/SCArray: Large-scale single-cell RNA-seq data manipulation with GDS files

Description

Opens a single-cell GDS file.

Usage

scOpen(gdsfn, readonly=TRUE, allow.duplicate=TRUE)

Arguments

gdsfn	the input file name
readonly	whether read-only or not
allow.duplicate	if TRUE, it is allowed to open a GDS file with read-only mode when it has been opened in the same R session

Value

Return an object of class SCArrayFileClass inherited from gds.class.

Author(s)

Xiuwen Zheng

See Also

scClose, scArray

Examples

# a GDS file for SingleCellExperiment
fn <- system.file("extdata", "LaMannoBrainData.gds", package="SCArray")

# open the GDS file
(f <- scOpen(fn))

# read a GDS file
cell.id <- read.gdsn(index.gdsn(f, "feature.id"))
samp.id <- read.gdsn(index.gdsn(f, "sample.id"))

# get a DelayedArray object
(cnt <- scArray(f, "counts"))

scClose(f)

zhengxwen/SCArray documentation built on Jan. 1, 2021, 1:54 p.m.