Get the ICA component data (stability, convergence, nMI) — get_ica_stability

Getter function to extract the ICA component data in terms of stability, convergence and normalised mutual information between the components. If not found will return NULL.

Usage

get_ica_stability_res(object)

Arguments

object: The class, see BulkCoExp().

Value

data.table with the ICA parameter data (if found. Otherwise NULL.)

Examples

# the stability table behind the ncomp choice
mat <- t(synthetic_signal_matrix()$mat)
obj <- BulkCoExp(mat, data.table::data.table(sample_id = rownames(mat)))
obj <- preprocess_bulk_coexp(obj, hvg = 0.3, .verbose = FALSE)
obj <- ica_processing(obj, .verbose = FALSE)
obj <- ica_evaluate_comp(
  obj,
  ica_type = "logcosh",
  ncomp_params = params_ica_ncomp(custom_seq = seq(2L, 20L, by = 2L)),
  .verbose = FALSE
)
head(get_ica_stability_res(obj))
#> Key: <no_components>
#>    no_components median_stability UQ_stability LQ_stability converged
#>            <int>            <num>        <num>        <num>     <num>
#> 1:             2        0.3341118    0.3371207    0.3311030      1.00
#> 2:             4        0.5896017    0.6422570    0.5311256      1.00
#> 3:             6        0.6287036    0.6477328    0.5436103      0.34
#> 4:             8        0.4903164    0.5704741    0.4185860      0.00
#> 5:            10        0.6038098    0.7605020    0.4277218      0.58
#> 6:            12        0.4654485    0.5977709    0.3903346      0.30
#>    norm_mutual_information combined_score
#>                      <num>          <num>
#> 1:              0.28908019      0.2375267
#> 2:              0.15172833      0.5001424
#> 3:              0.10588218      0.1911259
#> 4:              0.09540071      0.0000000
#> 5:              0.09111733      0.3182995
#> 6:              0.09419421      0.1264818