scfetch (version 0.5.0)

ExtractGEOExpSuppAll: 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
)

Value

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

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.