ExtractGEOExpSuppAll: Extract Raw Count Matrix from Supplementary Files or Fortmat...

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

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

Description

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

Usage

ExtractGEOExpSuppAll(
  acce,
  supp.idx = 1,
  timeout = 3600,
  supp.type = c("count", "10x"),
  out.folder = NULL,
  gene2feature = TRUE
)

Arguments

acce	GEO accession number.
supp.idx	The index of supplementary files to download. Default: 1.
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. Default: TURE.

Value

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

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