DownloadBam: Download bam.

In scfetch: Access and Format Single-Cell RNA-Seq Datasets from Public Resources

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 = ""
)

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: "".

Value

Dataframe contains failed runs or NULL.

Examples

## Not run: 
# 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"
)

## End(Not run)

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