DownloadSRA: Download SRA.
In scfetch: Access and Format Single-Cell RNA-Seq Datasets from Public Resources

DownloadSRA

R Documentation

Download SRA.

Description

Download SRA.

Usage

DownloadSRA(
  gsm.df,
  prefetch.path = NULL,
  out.folder = NULL,
  prefetch.paras = "-X 100G"
)

Arguments

`gsm.df`	Dataframe contains GSM and Run numbers, obtained from `ExtractRun`.
`prefetch.path`	Path to prefetch. Default: NULL (conduct automatic detection).
`out.folder`	Output folder. Default: NULL (current working directory).
`prefetch.paras`	Parameters for `prefetch`. Default: "-X 100G".

Value

Dataframe contains failed runs or NULL.

Examples

## Not run: 
# need users to provide the prefetch.path and out.folder
GSE186003.runs <- ExtractRun(acce = "GSE186003", platform = "GPL24247")
GSE186003.down <- DownloadSRA(
  gsm.df = GSE186003.runs, prefetch.path = "/path/to/prefetch",
  out.folder = "/path/to/output"
)

## End(Not run)

scfetch documentation built on Nov. 22, 2023, 1:09 a.m.