data-raw/fgsea.R

In acidgenomics/pfgsea: Acid Genomics GSEA

## nolint start
suppressPackageStartupMessages({
    library(devtools)
    library(usethis)
    library(goalie)
    library(basejump)
    library(DESeq2)
    library(DESeqAnalysis)
})
## nolint end
load_all()
## Restrict to 3 MB.
limit <- structure(3e6L, class = "object_size") # nolint
gr <- makeGRangesFromEnsembl(
    organism = "Homo sapiens",
    level = "genes",
    release = 100L,
    ignoreVersion = TRUE
)
gr <- as(gr, "GRanges")
gr <- gr[sort(names(gr))]
gr <- head(gr, n = 1000L)
gr <- droplevels2(gr)
mcols(gr) <- mcols(gr)[c("geneId", "geneName")]
## DESeqDataSet
dds <- makeExampleDESeqDataSet(n = length(gr), m = 12L)
colData(dds)[["treatment"]] <- as.factor(x = rep(c("C", "D"), each = 3L))
design(dds) <- ~ condition + treatment + condition:treatment
rowRanges(dds) <- gr
dds <- DESeq(dds)
dt <- varianceStabilizingTransformation(dds)
contrasts <- list(
    "condition_B_vs_A" = c(
        factor = "condition",
        numerator = "B",
        denominator = "A"
    ),
    "treatment_D_vs_C" = c(
        factor = "treatment",
        numerator = "D",
        denominator = "C"
    )
)
res <- Map(
    f = DESeq2::results,
    contrast = contrasts,
    MoreArgs = list("object" = dds)
)
## DESeqAnalysis
deseq <- DESeqAnalysis(
    data = dds,
    transform = dt,
    results = res,
    lfcShrink = NULL
)
## Just using hallmark in minimal example.
geneSetFiles <- prepareGeneSetFiles(
    dir = system.file(
        "extdata",
        "msigdb",
        "7.0",
        "msigdb_v7.0_GMTs",
        package = "AcidGSEA",
        mustWork = TRUE
    )
)
fgsea <- FgseaList(
    object = deseq,
    geneSetFiles = geneSetFiles
)
validObject(fgsea)
assert(
    object.size(fgsea) < limit,
    hasRows(fgsea[[1L]][[1L]]),
    is(metadata(fgsea)[["deseq"]], "DESeqAnalysis")
)
use_data(fgsea, overwrite = TRUE, compress = "xz")