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).

Examples

# pf.obj = GEOobj(acce = "GSE200257", platform = "GPL24676")
# count.mat = ExtractGEOExp(pf.obj, acce = "GSE200257", supp.idx = 1, down.supp = TRUE, supp.type = "10x",
#                           out.folder = "/path/to/output/folder")