relativeAb: Utility function to calculate relative abundances

In waldronlab/lefser: R implementation of the LEfSE method for microbiome biomarker discovery

Utility function to calculate relative abundances

Description

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)

Usage

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)
assay(relativeAb(se))

waldronlab/lefser documentation built on Nov. 1, 2024, 9:02 p.m.