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

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", "10xSingle"),
  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), 10x (cellranger output files in tar/gz supplementary files, contains barcodes, genes/features and matrix, e.g. GSE200257) and 10xSingle (cellranger output files in supplementary files directly, e.g. GSE236082). 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).