Accessor methods for the StructuralEnrichment S4 class.
Usage
structuralClassifications(x)
# S4 method for StructuralEnrichment
structuralClassifications(x)
# S4 method for StructuralEnrichment
explanatoryFeatures(x)
# S4 method for StructuralEnrichment
enrichmentResults(x)Examples
## Perform random forest on the example data
random_forest <- assigned_data %>%
metabolyseR::randomForest(
cls = 'class'
)
## Perform functional enrichment analysis
enrichment_results <- structuralEnrichment(
random_forest,
structural_classifications
)
## The m/z feature structural classifcations
structuralClassifications(enrichment_results)
#> # A tibble: 1,706 × 10
#> feature kingdom superclass class subclass `level 5` `level 6` `level 7`
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 n101.00585 Unknown NA NA NA NA NA NA
#> 2 n101.02399 Unknown NA NA NA NA NA NA
#> 3 n101.06042 Unknown NA NA NA NA NA NA
#> 4 n101.50757 Unknown NA NA NA NA NA NA
#> 5 n102.05566 Unknown NA NA NA NA NA NA
#> 6 n103.00333 Unknown NA NA NA NA NA NA
#> 7 n103.03965 Unknown NA NA NA NA NA NA
#> 8 n103.95837 Unknown NA NA NA NA NA NA
#> 9 n104.03495 Unknown NA NA NA NA NA NA
#> 10 n105.01896 Unknown NA NA NA NA NA NA
#> # ℹ 1,696 more rows
#> # ℹ 2 more variables: `level 8` <chr>, `level 9` <chr>
## Access the explanatory features used for structural enrichment analysis
explanatoryFeatures(enrichment_results)
#> # A tibble: 153 × 5
#> response comparison feature metric value
#> <chr> <chr> <chr> <chr> <dbl>
#> 1 class ABR1~ABR5~ABR6~BD21 n267.05255 C12H12O7 [M-H]1- false_p… 5.13e-17
#> 2 class ABR1~ABR5~ABR6~BD21 p130.04956 false_p… 1.92e-13
#> 3 class ABR1~ABR5~ABR6~BD21 n176.93581 CH3O6P [M+Cl]1- false_p… 2.65e-12
#> 4 class ABR1~ABR5~ABR6~BD21 n295.10519 false_p… 2.65e-12
#> 5 class ABR1~ABR5~ABR6~BD21 n371.10074 false_p… 2.65e-12
#> 6 class ABR1~ABR5~ABR6~BD21 n447.09634 C18H24O11S [M-H]1- false_p… 3.43e-11
#> 7 class ABR1~ABR5~ABR6~BD21 n385.11682 false_p… 4.15e-10
#> 8 class ABR1~ABR5~ABR6~BD21 n439.08383 C26H16O7 [M-H]1- false_p… 4.15e-10
#> 9 class ABR1~ABR5~ABR6~BD21 n88.98757 C2H2O4 [M-H]1- false_p… 4.15e-10
#> 10 class ABR1~ABR5~ABR6~BD21 n101.02399 false_p… 4.66e- 9
#> # ℹ 143 more rows
## Access the structral enrichment analysis results
enrichmentResults(enrichment_results)
#> # A tibble: 46 × 15
#> response comparison level classification Explanatory & in cla…¹
#> <chr> <chr> <chr> <chr> <int>
#> 1 class ABR1~ABR5~ABR6~BD21 kingdom Organic compo… 41
#> 2 class ABR1~ABR5~ABR6~BD21 superclass Benzenoids 9
#> 3 class ABR1~ABR5~ABR6~BD21 class Benzene and s… 5
#> 4 class ABR1~ABR5~ABR6~BD21 class Organic phosp… 5
#> 5 class ABR1~ABR5~ABR6~BD21 superclass Phenylpropano… 4
#> 6 class ABR1~ABR5~ABR6~BD21 subclass Organic phosp… 4
#> 7 class ABR1~ABR5~ABR6~BD21 subclass Non-metal pho… 3
#> 8 class ABR1~ABR5~ABR6~BD21 subclass Dicarboxylic … 4
#> 9 class ABR1~ABR5~ABR6~BD21 class Coumarins and… 2
#> 10 class ABR1~ABR5~ABR6~BD21 class Flavonoids 2
#> # ℹ 36 more rows
#> # ℹ abbreviated name: ¹`Explanatory & in class`
#> # ℹ 10 more variables: `Not explanatory & in class` <int>,
#> # `Explanatory & not in class` <int>, `Not explanatory & not in class` <int>,
#> # estimate <dbl>, p.value <dbl>, adjusted.p.value <dbl>, conf.low <dbl>,
#> # conf.high <dbl>, method <chr>, alternative <chr>