scml: SCML: spike-in-based calibration to total microbial load

In waldronlab/MicrobiomeBenchmarkData: Datasets for benchmarking in microbiome research

SCML: spike-in-based calibration to total microbial load

Description

The scml function applies the spike-in-based calibration to total microbial load (SCML) method to

Usage

scml(tse, bac = c("s", "r", "a"))

Arguments

tse	A treeSummarizedExperiment from the getBenchmarkData function.
bac	A character. One of the following options: s = Salinibacter ruber (AF323500), r = Rhizobium radiobacter (AB247615), a, = Alicyclobacillus acidiphilus (AB076660)

Value

A TreeSummarizedExperiment with SCML data instead of counts.

Examples

tse <- getBenchmarkData("Stammler_2016_16S_spikein", dryrun = FALSE)[[1]]
tseSCML <- scml(tse, bac = "s")

waldronlab/MicrobiomeBenchmarkData documentation built on Oct. 31, 2024, 3:43 a.m.