scfetch (version 0.5.0)

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

Description

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
)

Value

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

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.