buildRaw: buildRaw gets the raw data in SummarizedExperiment format

In flaviusb/homosapienDEE2CellScore: Example Data Package for CellScore

buildRaw gets the raw data in SummarizedExperiment format

Description

This function gets the raw Data from dee2 and packages it in a SummarizedExperiment

Usage

buildRaw(
  species = "hsapiens",
  accessions = unique(cols$SRR_accession),
  quiet = TRUE,
  metadata = getDEE2Metadata(species, quiet = quiet)
)

Arguments

species	The species to fetch data for; default is "hsapiens".
accessions	Which sample ids to download from DEE2 (we refer to these as accessions); default is derived from 'hsapiens_colData.csv' in this package. For subsets, you can see the internal 'cols' objects 'SRR_accession' member.
quiet	Whether to suppress notification output where possible; default TRUE.
metadata	If you have already downloaded metadata for the species, you can pass it in here. Otherwise the metadata will be downloaded.

Value

Returns a SummarizedExperiment object containing raw data downloaded from dee2.

Examples

# To get a few accessions and package them into a SummarizedExperiment
accessions_of_interest <- buildRaw(accessions=as.list(unique(cols$SRR_accession)[c(1,3)]))

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