Utility function to calculate relative abundances

Source: R/utils.R

The function calculates the column totals and divides each value within the column by the respective column total.

This function calculates the relative abundance of each feature in the SummarizedExperiment object containing count data, expressed as counts per million (CPM)

relativeAb(se, assay = 1L)

Arguments

se

A SummarizedExperiment object with counts

assay

The i-th assay matrix in the SummarizedExperiment ('relab'; default 1).

Value

returns a new SummarizedExperiment object with counts per million calculated and added as a new assay named rel_abs.

Examples


se <- SummarizedExperiment(
    assays = list(
        counts = matrix(
            rep(1, 4), ncol = 1, dimnames = list(LETTERS[1:4], "SAMP")
        )
    )
)
assay(se)
#>   SAMP
#> A    1
#> B    1
#> C    1
#> D    1
assay(relativeAb(se))
#>     SAMP
#> A 250000
#> B 250000
#> C 250000
#> D 250000