In LTLA/celldex: Index of Reference Cell Type Datasets

From ExperimentHub to gypsum

knitr::opts_chunk$set(error=FALSE, message=FALSE)

Pulling assets from ExperimentHub.

library(ExperimentHub)
hub <- ExperimentHub()
prefix <- "celldex/dmap/"
norm.hub <- hub[hub$rdatapath==paste0(prefix, "1.0.0/logcounts.rds")]
stopifnot(nrow(norm.hub) == 1L)
norm <- norm.hub[[1]]
str(norm)
coldata.hub <- hub[hub$rdatapath==paste0(prefix, "1.2.0/coldata.rds")] # fixed umlaut.
stopifnot(nrow(coldata.hub) == 1L)
coldata <- coldata.hub[[1]]
coldata

Attaching ontology mappings.

path <- system.file("mapping", "novershtern.tsv", package="celldex", mustWork=TRUE)
src <- read.delim(path, header=FALSE, stringsAsFactors=FALSE)

m <- match(coldata$label.fine, src[,1])
stopifnot(all(!is.na(m))) # sanity check

matched <- src[m, 2]
matched[matched==""] <- NA_character_
coldata$label.ont <- matched
coldata

Assembling some metadata.

meta <- list(
    title="Bulk microarray expression of sorted hematopoietic cells from Novershtern et al.",
    description=paste(c(
        "Log-normalized expression values for 211 human microarray samples from Novershtern et al. (2011).",
        "A matrix of RMA-normalized expression values was downloaded from GEO using the accession GSE24759.",
        "For genes with multiple probes, only the probe with the highest average expression was retained.",
        "Samples were annotated to 16 main cell types (`label.main`):",
        "- Basophils",
        "- B cells",
        "- CMPs",
        "- Dendritic cells",
        "- Eosinophils",
        "- Erythroid cells",
        "- GMPS",
        "- Granulocytes",
        "- HSCs",
        "- Megakaryocytes",
        "- MEPs",
        "- Monocytes",
        "- NK cells",
        "- NK T cells",
        "- CD8+ T cells",
        "- CD4+ T cells",
        "",
        "These labels were further resolved into 38 fine cell types (`label.fine`):",
        "- Basophils",
        "- Naive B cells",
        "- Mature B cells class able to switch",
        "- Mature B cells",
        "- Mature B cells class switched",
        "- Common myeloid progenitors",
        "- Plasmacytoid Dendritic Cells",
        "- Myeloid Dendritic Cells",
        "- Eosinophils",
        "- Erythroid_CD34+ CD71+ GlyA-",
        "- Erythroid_CD34- CD71+ GlyA-",
        "- Erythroid_CD34- CD71+ GlyA+",
        "- Erythroid_CD34- CD71lo GlyA+",
        "- Erythroid_CD34- CD71- GlyA+",
        "- Granulocyte/monocyte progenitors",
        "- Colony Forming Unit-Granulocytes",
        "- Granulocyte (Neutrophilic Metamyelocytes)",
        "- Granulocyte (Neutrophils)",
        "- Hematopoietic stem cells_CD133+ CD34dim",
        "- Hematopoietic stem cell_CD38- CD34+",
        "- Colony Forming Unit-Megakaryocytic",
        "- Megakaryocytes",
        "- Megakaryocyte/erythroid progenitors",
        "- Colony Forming Unit-Monocytes",
        "- Monocytes",
        "- Mature NK cells_CD56- CD16+ CD3-",
        "- Mature NK cells_CD56+ CD16+ CD3-",
        "- Mature NK cells_CD56- CD16- CD3-",
        "- NK T cells",
        "- Early B cells",
        "- Pro B cells",
        "- CD8+ Effector Memory RA",
        "- Naive CD8+ T cells",
        "- CD8+ Effector Memory",
        "- CD8+ Central Memory",
        "- Naive CD4+ T cells",
        "- CD4+ Effector Memory",
        "- CD4+ Central Memory",
        "",
        "The fine types have also been mapped to the Cell Ontology (`label.ont`)."
    ), collapse="\n"),
    taxonomy_id="9606",
    genome=character(0), # dunno, it doesn't say.
    sources=list(
        list(provider="PubMed", id="21241896"),
        list(provider="GEO", id="GSE24759"),
        list(provider="ExperimentHub", id=norm.hub$ah_id),
        list(provider="ExperimentHub", id=coldata.hub$ah_id)
    ),
    maintainer_name="Jared Andrews",
    maintainer_email="[e-mail]"
)

Saving it to disk.

library(celldex)
path <- "2024-02-26_output"
saveReference(norm, coldata, path, meta)

LTLA/celldex documentation built on April 29, 2024, 4:34 p.m.