writeOutSEZip: writeOutSEZip writes out a SummarizedExperiment into a zip...

In flaviusb/homosapienDEE2CellScore: Example Data Package for CellScore

writeOutSEZip writes out a SummarizedExperiment into a zip file

Description

This function writes out a SummarizedExperiment into a group of zipped csvs, with a manifest.csv It is designed for use in persisting the SummarizedExperiments generated by this data package, for upload to ExperimentHub, so it is not built robustly.

Usage

writeOutSEZip(
  the_summarized_experiment,
  filename_base = "SE_out",
  filename_ext = ".csv",
  filenames = list(metadata = paste(filename_base, "_metadata", filename_ext, sep = ""),
    assay_counts = paste(filename_base, "_assay_counts", filename_ext, sep = ""),
    assay_calls = paste(filename_base, "_assay_calls", filename_ext, sep = ""), colData =
    paste(filename_base, "_colData", filename_ext, sep = ""), rowData =
    paste(filename_base, "_rowData", filename_ext, sep = "")),
  zip_name = paste(filename_base, ".zip", sep = "")
)

Arguments

the_summarized_experiment	A SummarizedExperiment
filename_base	The default base name to use for each of the generated files within the zip file
filename_ext	The default extension to use for each of the generated files within the zip file
filenames	A tagged list of filenames for the files inside the zip file: 'metadata', 'assay_counts', 'assay_calls', 'colData', 'rowData'.
zip_name	The name of the generated zip file.

Value

The status value returned by the external command invoked to create the zip file, invisibly.

Examples

# First, we download a few accessions of interest into a SummarizedExperiment
accessions_of_interest <- buildData(
  accessions=as.list(unique(cols$SRR_accession)[c(1,3)]), write_files=FALSE,
  build_raw=TRUE, build_deseq2=FALSE, build_tsne=FALSE, build_rank=FALSE,
  generate_qc_pass=FALSE)$qc_warn_raw
# Then we write them out to a zip file for later
writeOutSEZip(accessions_of_interest, filename_base="InterestingAccessionsForLater")

flaviusb/homosapienDEE2CellScore documentation built on April 11, 2024, 1:47 p.m.