ExtractGEOExp: Extract Raw Count Matrix or Fortmat Supplementary Files to...

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

Extract Raw Count Matrix or Fortmat Supplementary Files to 10x.

Description

Extract Raw Count Matrix or Fortmat Supplementary Files to 10x.

Usage

ExtractGEOExp(
  pf.obj,
  acce,
  supp.idx = 1,
  down.supp = FALSE,
  timeout = 3600,
  supp.type = c("count", "10x"),
  out.folder = NULL,
  gene2feature = TRUE
)

Arguments

pf.obj	GEO object of platform.
acce	GEO accession number.
supp.idx	The index of supplementary files to download. Default: 1.
down.supp	Logical value, whether to download supplementary files to create count matrix. If TRUE, always download supplementary files. If FALSE, use ExpressionSet (If contains non-integer or emoty, download supplementary files automatically). Default: FALSE.
timeout	Timeout for download.file. Default: 3600.
supp.type	The type of downloaded supplementary files, choose from count (count matrix file or single count matrix file) and 10x (cellranger output files, contains barcodes, genes/features and matrix). Default: count.
out.folder	Output folder to save 10x files. Default: NULL (current working directory).
gene2feature	Logical value, whether to rename genes.tsv.gz to features.tsv.gz. Default: TRUE.

Value

Count matrix (supp.type is count) or NULL (supp.type is 10x).

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