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/hpca/"
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, "1.0.0/coldata.rds")]
stopifnot(nrow(coldata.hub) == 1L)
coldata <- coldata.hub[[1]]
coldata

Attaching ontology mappings.

path <- system.file("mapping", "hpca.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="Microarray data from the Human Primary Cell Atlas",
    description=paste(c(
        "Log-normalized expression values for 713 microarray samples from the Human Primary Cell Atlas (HPCA) (Mabbott et al., 2013).",
        "These 713 samples were processed and normalized as described in Aran, Looney and Liu et al. (2019).",
        "Each sample was assigned to one of 37 main cell types (`label.main`) and 157 subtypes (`label.fine`).",
        "The subtypes 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="24053356"),
        list(provider="PubMed", id="30643263"),
        list(provider="GitHub", id="dviraran/SingleR", version="adc4a0e4d5cfa79db18f3821f51a02cbd6484710"),
        list(provider="ExperimentHub", id=norm.hub$ah_id),
        list(provider="ExperimentHub", id=coldata.hub$ah_id)
    ),
    maintainer_name="Friederike Dündar",
    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.