ParseGEO: Download Matrix from GEO and Load to Seurat.

In scfetch: Access and Format Single-Cell RNA-Seq Datasets from Public Resources

Download Matrix from GEO and Load to Seurat.

Description

Download Matrix from GEO and Load to Seurat.

Usage

ParseGEO(
  acce,
  platform = NULL,
  down.supp = FALSE,
  supp.idx = 1,
  timeout = 3600,
  data.type = c("sc", "bulk"),
  supp.type = c("count", "10x"),
  out.folder = NULL,
  gene2feature = TRUE,
  merge = TRUE,
  ...
)

Arguments

acce	GEO accession number.
platform	Platform information/field. Disable when down.supp is TRUE. Default: NULL (disable).
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 empty, download supplementary files automatically). Default: FALSE.
supp.idx	The index of supplementary files to download. This should be consistent with platform. Default: 1.
timeout	Timeout for download.file. Default: 3600.
data.type	The data type of the dataset, choose from "sc" (single-cell) and "bulk" (bulk). Default: "sc".
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.
merge	Logical value, whether to merge Seurat list when there are multiple 10x files (supp.type is 10x). Default: FALSE.
...	Parameters for getGEO.

Value

If data.type is "sc", return Seurat object (if merge is TRUE) or Seurat object list (if merge is FALSE). If data.type is "bulk", return count matrix.

Examples

## Not run: 
# the supp files are count matrix
GSE94820.seu <- ParseGEO(acce = "GSE94820", down.supp = TRUE, supp.idx = 1, supp.type = "count")
# the supp files are cellranger output files: barcodes, genes/features and matrix
# need users to provide the output folder
GSE200257.seu <- ParseGEO(
  acce = "GSE200257", down.supp = TRUE, supp.idx = 1, supp.type = "10x",
  out.folder = "/path/to/output/folder"
)

## End(Not run)

scfetch documentation built on Nov. 22, 2023, 1:09 a.m.