Convert a VISTA object to a DESeqDataSet — as_deseq

Builds a DESeq2::DESeqDataSet from the raw counts retained in a VISTA object, so an analysis can be continued or re-run with DESeq2 directly.

Usage

as_deseq_dataset(x, design = NULL)

Arguments

x: A VISTA object carrying a raw counts assay.
design: A model formula. Defaults to ~ <group column> using the grouping column stored in the object.

Value

A DESeqDataSet.

Details

This is deliberately explicit rather than making DESeq2::DESeqDataSet(v, design) work implicitly: the inherited SummarizedExperiment method would pick up whichever assay comes first, which is norm_counts, and fail because those values are not integers.

Counts are rounded to integers, as DESeq2 requires.

Examples

v <- example_vista()
if (requireNamespace("DESeq2", quietly = TRUE)) {
  dds <- as_deseq_dataset(v)
  class(dds)
}
#> converting counts to integer mode
#> [1] "DESeqDataSet"
#> attr(,"package")
#> [1] "DESeq2"