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).

Examples

# exp.data = ExtractGEOExpSuppAll(acce = "GSE200257", supp.idx = 1, supp.type = "10x",
#                                 out.folder = "/path/to/output/folder")