Automatic Imputation — auto_impute • glyclean

This function automatically selects and applies a deterministic default imputation method by sample count and experiment type. Quality Control (QC) samples are inspected for workflow consistency, but they are not used to benchmark or select the imputation method.

Usage

auto_impute(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 QC sample information. 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 imputed experiment.

Details

The automatic strategy uses these defaults:

n_samples < 30: impute_min_prob() for glycomics and glycoproteomics.
30 <= n_samples <= 100: impute_bpca() for glycomics and impute_min_prob() for glycoproteomics.
n_samples > 100: impute_miss_forest() for glycomics and impute_bpca() for glycoproteomics.

Other experiment types use the glycoproteomics defaults as a conservative fallback. impute_sample_min() and impute_half_sample_min() remain available for manual use, but they are not selected automatically.

Examples

library(glyexp)
exp_imputed <- auto_impute(real_experiment)
#> ℹ Imputation method: `impute_min_prob()`
#> ℹ Reason: default for "glycoproteomics" with n_samples < 30.