Run DESeq2 on a multiOmicDataSet — run_deseq2 • MOSuite

Run DESeq2 on a multiOmicDataSet

Usage

run_deseq2(moo, design, ...)

Arguments

moo: multiOmicDataSet object
design: model formula for experimental design. Columns must exist in meta_dat.
...: remaining variables are forwarded to DESeq2::DESeq().

Value

multiOmicDataSet object with DESeq2 slot filled

See also

Other moo methods: batch_correct_counts(), clean_raw_counts(), diff_counts(), filter_counts(), filter_diff(), normalize_counts(), plot_corr_heatmap(), plot_expr_heatmap(), plot_histogram(), plot_pca(), plot_read_depth(), set_color_pal()

Examples

if (FALSE) { # \dontrun{
moo <- create_multiOmicDataSet_from_files(
  system.file("extdata", "sample_metadata.tsv.gz",
    package = "MOSuite"
  ),
  system.file("extdata",
    "RSEM.genes.expected_count.all_samples.txt.gz",
    package = "MOSuite"
  )
) %>% filter_counts()
moo <- run_deseq2(moo, ~condition)
} # }