Automatic Normalization — auto_normalize • glyclean

This function automatically applies a deterministic default normalization method based on experiment type. Quality Control (QC) samples are not used to benchmark, select, or report normalization behavior.

Usage

auto_normalize(exp, group_col = "group", qc_name = "QC", to_try = NULL)

Arguments

exp: An glyexp::experiment().
group_col: The column name in sample_info for groups. Default is "group". Can be NULL when no group information is available.
qc_name: This function no longer uses this argument. This parameter is ignored and will be removed in a future release.
to_try: This parameter is no longer used and will be removed in a future release. The automatic strategy is now deterministic and does not require user-specified methods to try.

Value

The normalized experiment.

Details

The automatic strategy uses these defaults:

glycomics: normalize_total_area().
glycoproteomics: normalize_median().
missing or other experiment types: normalize_median().

Examples

library(glyexp)
exp_normed <- auto_normalize(real_experiment)
#> ℹ Normalization method: `normalize_median()`
#> ℹ Reason: default for "glycoproteomics".