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Run multiple normalization methods from a baseline assay

Source: R/Normalization_Metrics.R
nm_run_normalizations.Rd

Takes a SummarizedExperiment with a log2-scale assay and applies each requested normalization method, returning a new SE with one assay per method.

Usage

nm_run_normalizations(
  se,
  assay_name = "log2",
  methods = "all",
  method_args = list(),
  include_baseline = TRUE,
  verbose = TRUE
)

Arguments

se

SummarizedExperiment with at least one log2-scale assay.

assay_name

Name of the baseline assay to normalize from. Default "log2".

methods

Character vector of method names, or "all" for all 12 benchmark methods. Default "all".

method_args

Named list of per-method arguments. E.g. list(cycloess = list(method = "fast", span = 0.8)).

include_baseline

Logical. Include the baseline assay in the output SE. Default TRUE.

verbose

Logical. Print progress messages. Default TRUE.

Value

SummarizedExperiment with one assay per successfully normalized method (plus baseline if include_baseline = TRUE).

Examples

data(nadia_dia)
se <- nm_prepare_se(nadia_dia, verbose = FALSE)
se_bench <- nm_run_normalizations(se, methods = c("cycloess", "quantile", "MAD"),
                                  verbose = FALSE)
SummarizedExperiment::assayNames(se_bench)
#> [1] "log2"     "cycloess" "quantile" "MAD"