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Prepare a SummarizedExperiment from a proteomics_data object

Source: R/Normalization_Metrics.R
nm_prepare_se.Rd

Convenience wrapper that extracts metadata and protein data from a proteomics_data object (from any of the preprocess_*() functions), performs zero-to-NA conversion, protein filtering, and returns a SE with assays "raw" and "log2" – ready for nm_run_normalizations() or normalization_metrics(..., methods = "all").

Usage

nm_prepare_se(
  preprocessing,
  min_reps = NULL,
  min_groups = 1,
  covariate_df = NULL,
  verbose = TRUE
)

Arguments

preprocessing

A proteomics_data object, from any of the preprocess_*() functions.

min_reps

Minimum replicates with non-NA values per group for protein filtering. If NULL, auto-computed as half the smallest group. Default NULL.

min_groups

Minimum groups meeting min_reps (default: 1).

covariate_df

Optional covariate data.frame for paired designs (must contain a Column column). Default NULL.

verbose

Logical. Print progress messages. Default TRUE.

Value

SummarizedExperiment with assays "raw" and "log2".

Details

Internally calls normalize_proteomics() with norm_method = "log2" (no additional normalization).

Examples

data(nadia_dia)
se <- nm_prepare_se(nadia_dia, verbose = FALSE)
dim(se)
#> [1] 1997   12
SummarizedExperiment::assayNames(se)
#> [1] "raw"  "log2"