scfetch (version 0.5.0)

DownloadBam: Download bam.

Description

Download bam.

Usage

DownloadBam(
  gsm.df,
  bam.type = c("10x", "other"),
  prefetch.path = NULL,
  samdump.path = NULL,
  out.folder = NULL,
  prefetch.paras = "-X 100G",
  samdump.paras = ""
)

Value

Dataframe contains failed runs or NULL.

Arguments

gsm.df

Dataframe contains GSM and Run numbers, obtained from ExtractRun.

bam.type

The source of bam files to download, choose from 10x (e.g. CellRanger) or other. Default: 10x.

prefetch.path

Path to prefetch. Default: NULL (conduct automatic detection).

samdump.path

Path to sam-dump, used when bam.type is other. Default: NULL (conduct automatic detection).

out.folder

Output folder. Default: NULL (current working directory).

prefetch.paras

Parameters for prefetch. This should not contain --type or -T values. Default: "-X 100G".

samdump.paras

Parameters for sam-dump. Default: "".

Examples

if (FALSE) {
# need users to provide prefetch.path
GSE138266.runs <- ExtractRun(acce = "GSE138266", platform = "GPL18573")
GSE138266.down <- DownloadBam(
  gsm.df = GSE138266.runs, bam.type = "10x",
  prefetch.path = "/path/to/prefetch",
  out.folder = "/path/to/output"
)
}