Download Matrix from GEO and Load to Seurat/DESeq2.

Usage

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

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), 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.
merge: Logical value, whether to merge Seurat list when there are multiple 10x files (supp.type is 10x). Default: FALSE.
meta.data: Dataframe contains sample information for DESeqDataSet, use when data.type is bulk. Default: NULL.
fmu: Column of meta.data contains group information. Default: NULL.
...: 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 DESeqDataSet.

Examples

if (FALSE) {
# 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"
)
# need users to provide the output folder
GSE236082.seu <- ParseGEO(
  acce = "GSE236082", down.supp = TRUE, supp.type = "10xSingle",
  out.folder = "/path/to/output/folder"
)
}