Convert a SummarizedExperiment to a metaXpressStudy

Wraps any SummarizedExperiment (including DESeqDataSet and RangedSummarizedExperiment objects, e.g. from recount3 or tximeta) as a metaXpressStudy so it can enter the metaXpress pipeline. as(se, "metaXpressStudy") calls this with defaults.

Usage

mx_from_se(
  se,
  assay_name = "counts",
  condition_col = "condition",
  accession = NULL,
  organism = NULL
)

Arguments

se

A SummarizedExperiment or subclass.

assay_name

Name of the assay holding raw counts. Defaults to "counts", falling back to the first assay if absent.

condition_col

Name of the colData column holding case/control labels; copied to condition if different.

accession

Accession ID. Defaults to metadata(se)$accession if present, otherwise "local".

organism

Species name. Defaults to metadata(se)$organism if present, otherwise "Homo sapiens".

Value

A metaXpressStudy object.

See also

metaXpressStudy

Examples

se <- SummarizedExperiment::SummarizedExperiment(
  assays  = list(counts = matrix(rpois(24, 100), nrow = 4,
    dimnames = list(paste0("GENE", 1:4), paste0("S", 1:6)))),
  colData = data.frame(dex = rep(c("untrt", "trt"), each = 3))
)
study <- mx_from_se(se, condition_col = "dex")