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Calculate counts-per-million (CPM) on raw counts in a multiOmicDataSet

Source: R/counts.R
calc_cpm.Rd

Calculate counts-per-million (CPM) on raw counts in a multiOmicDataSet

Usage

calc_cpm(moo, ...)

Arguments

moo

multiOmicDataSet object

...

additional arguments to pass to edgeR::cpm()

Value

multiOmicDataSet with cpm-transformed counts

See also

Other moo methods: batch_correct_counts(), clean_raw_counts(), diff_counts(), extract_counts(), filter_counts(), filter_diff(), normalize_counts(), plot_corr_heatmap(), plot_expr_heatmap(), plot_histogram(), plot_pca(), plot_pca_2d(), plot_pca_3d(), plot_read_depth(), plot_venn_diagram(), plot_volcano_enhanced(), plot_volcano_summary(), run_deseq2(), set_color_pal(), set_default_colors()

Examples

sample_meta <- data.frame(
  sample_id = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"),
  condition = factor(
    c("knockout", "knockout", "wildtype", "wildtype"),
    levels = c("wildtype", "knockout")
  )
)
moo <- create_multiOmicDataSet_from_dataframes(sample_meta, gene_counts) |>
  calc_cpm()
head(moo@counts$cpm)
#>              gene_id KO_S3 KO_S4 WT_S1 WT_S2
#> 1 ENSG00000121410.11     0     0     0     0
#> 2  ENSG00000268895.5     0     0     0     0
#> 3 ENSG00000148584.15     0     0     0     0
#> 4 ENSG00000175899.14     0     0     0     0
#> 5  ENSG00000245105.3     0     0     0     0
#> 6 ENSG00000166535.20     0     0     0     0