inst/scripts/2.4.0/make-wu-kidney-metadata.R

In drisso/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

write.csv(file="../../extdata/2.4.0/metadata-wu-kidney.csv", 
    data.frame(
        Title = sprintf("Wu %s mouse kidney %s", 
            rep(c("healthy", "diseased"), each=2),
            rep(c("counts", "colData"), 2)),
        Description = sprintf("%s for %s in the Wu mouse kidney single-nucleus RNA-seq dataset", 
            rep(c("Count matrix", "Per-cell metadata"), 2),
            rep(c("healthy tissue", "fibrotic tissue"), each=2)),
        RDataPath = file.path("scRNAseq", "wu-kidney", "2.4.0", 
            paste0(c("counts-healthy", "coldata-healthy", "counts-disease", "coldata-disease"), ".rds")),
        BiocVersion="3.12",
        Genome="mm10",
        SourceType="TSV",
        SourceUrl="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119531",
        SourceVersion=c(
            "GSE119531_Healthy.combined.dge.txt.gz",
            "GSE119531_Healthy.combined.cell.annotation.txt.gz",
            "GSE119531_UUO.dge.txt.gz",
            "GSE119531_UUO.cell.annotation.txt.gz"
        ),
        Species="Mus musculus",
        TaxonomyId="10090",
        Coordinate_1_based=NA,
        DataProvider="GEO",
        Maintainer="Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>",
        RDataClass=c("dgCMatrix", "data.frame", "dgCMatrix", "data.frame"),
        DispatchClass="Rds",
        stringsAsFactors = FALSE
    ),
    row.names=FALSE)