scfetch (version 0.5.0)

DownloadSRA: Download SRA.

Description

Download SRA.

Usage

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

Value

Dataframe contains failed runs or NULL.

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".

Examples

if (FALSE) {
# 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"
)
}