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

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|A1BG     0     0     0     0
#> 2 ENSG00000268895.5|A1BG-AS1     0     0     0     0
#> 3    ENSG00000148584.15|A1CF     0     0     0     0
#> 4     ENSG00000175899.14|A2M     0     0     0     0
#> 5  ENSG00000245105.3|A2M-AS1     0     0     0     0
#> 6   ENSG00000166535.20|A2ML1     0     0     0     0