For a prep Recipe adds a consensus strategy to use for result extraction.
Usage
bake(
rec,
count_cutoff = NULL,
weights = NULL,
exclude = NULL,
id = rand_id("bake")
)Arguments
- rec
A PrepRecipe object. The step will be added to the sequence of operations for this Recipe.
- count_cutoff
Indicates the minimum number of methods in which an OTU must be present (Default: NULL). If
count_cutoffisNULL, it is set tolength(steps_ids(rec, "da")) - length(exclude).- weights
Named numeric vector with the weight for each method.
- exclude
Method ids to exclude.
- id
A character string that is unique to this step to identify it.
Examples
data(test_prep_rec)
## Require agreement among all differential-abundance methods
cool(bake(test_prep_rec))
#> ℹ Baking with count_cutoff = 2
#> # A tibble: 16 × 9
#> taxa_id taxa contrast_id comparison contrast_type var effect method_count
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl>
#> 1 Otu_119 Alist… RiskGroup2… RiskGroup… main Risk… down 2
#> 2 Otu_119 Alist… RiskGroup2… RiskGroup… main Risk… up 2
#> 3 Otu_125 Parab… RiskGroup2… RiskGroup… main Risk… down 2
#> 4 Otu_259 Copro… RiskGroup2… RiskGroup… main Risk… up 2
#> 5 Otu_262 Dorea RiskGroup2… RiskGroup… main Risk… up 2
#> 6 Otu_262 Dorea RiskGroup2… RiskGroup… main Risk… down 2
#> 7 Otu_332 Caten… RiskGroup2… RiskGroup… main Risk… up 2
#> 8 Otu_332 Caten… RiskGroup2… RiskGroup… main Risk… down 2
#> 9 Otu_35 Colli… RiskGroup2… RiskGroup… main Risk… up 2
#> 10 Otu_354 Firmi… RiskGroup2… RiskGroup… main Risk… up 2
#> 11 Otu_78 Bacte… RiskGroup2… RiskGroup… main Risk… down 2
#> 12 Otu_78 Bacte… RiskGroup2… RiskGroup… main Risk… up 2
#> 13 Otu_82 Barne… RiskGroup2… RiskGroup… main Risk… down 2
#> 14 Otu_88 Odori… RiskGroup2… RiskGroup… main Risk… down 2
#> 15 Otu_88 Odori… RiskGroup2… RiskGroup… main Risk… up 2
#> 16 Otu_96 Prevo… RiskGroup2… RiskGroup… main Risk… up 2
#> # ℹ 1 more variable: methods <chr>
## Retain taxa detected by at least one method
cool(bake(test_prep_rec, count_cutoff = 1))
#> ℹ Baking with count_cutoff = 1
#> # A tibble: 46 × 9
#> taxa_id taxa contrast_id comparison contrast_type var effect method_count
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl>
#> 1 Otu_1 Metha… RiskGroup2… RiskGroup… main Risk… up 1
#> 2 Otu_119 Alist… RiskGroup2… RiskGroup… main Risk… down 2
#> 3 Otu_119 Alist… RiskGroup2… RiskGroup… main Risk… up 2
#> 4 Otu_125 Parab… RiskGroup2… RiskGroup… main Risk… down 2
#> 5 Otu_125 Parab… RiskGroup2… RiskGroup… main Risk… up 1
#> 6 Otu_231 Eubac… RiskGroup2… RiskGroup… main Risk… up 1
#> 7 Otu_255 Blaut… RiskGroup2… RiskGroup… main Risk… up 1
#> 8 Otu_259 Copro… RiskGroup2… RiskGroup… main Risk… up 2
#> 9 Otu_259 Copro… RiskGroup2… RiskGroup… main Risk… down 1
#> 10 Otu_262 Dorea RiskGroup2… RiskGroup… main Risk… up 2
#> # ℹ 36 more rows
#> # ℹ 1 more variable: methods <chr>
## Exclude a method from the consensus
method_ids <- steps_ids(test_prep_rec, "da")
cool(bake(test_prep_rec, exclude = method_ids[1]))
#> ℹ Baking with count_cutoff = 1
#> Excluding "maaslin__Welsh_cake".
#> # A tibble: 36 × 9
#> taxa_id taxa contrast_id comparison contrast_type var effect method_count
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl>
#> 1 Otu_1 Metha… RiskGroup2… RiskGroup… main Risk… up 1
#> 2 Otu_119 Alist… RiskGroup2… RiskGroup… main Risk… down 1
#> 3 Otu_119 Alist… RiskGroup2… RiskGroup… main Risk… up 1
#> 4 Otu_125 Parab… RiskGroup2… RiskGroup… main Risk… down 1
#> 5 Otu_231 Eubac… RiskGroup2… RiskGroup… main Risk… up 1
#> 6 Otu_255 Blaut… RiskGroup2… RiskGroup… main Risk… up 1
#> 7 Otu_259 Copro… RiskGroup2… RiskGroup… main Risk… up 1
#> 8 Otu_262 Dorea RiskGroup2… RiskGroup… main Risk… up 1
#> 9 Otu_262 Dorea RiskGroup2… RiskGroup… main Risk… down 1
#> 10 Otu_332 Caten… RiskGroup2… RiskGroup… main Risk… up 1
#> # ℹ 26 more rows
#> # ℹ 1 more variable: methods <chr>
## Give the first method twice the weight of the others
weights <- setNames(rep(1, length(method_ids)), method_ids)
weights[1] <- 2
cool(bake(test_prep_rec, weights = weights))
#> ℹ Baking with count_cutoff = 2
#> # A tibble: 26 × 9
#> taxa_id taxa contrast_id comparison contrast_type var effect method_count
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl>
#> 1 Otu_119 Alist… RiskGroup2… RiskGroup… main Risk… down 3
#> 2 Otu_119 Alist… RiskGroup2… RiskGroup… main Risk… up 3
#> 3 Otu_125 Parab… RiskGroup2… RiskGroup… main Risk… down 3
#> 4 Otu_125 Parab… RiskGroup2… RiskGroup… main Risk… up 2
#> 5 Otu_259 Copro… RiskGroup2… RiskGroup… main Risk… up 3
#> 6 Otu_259 Copro… RiskGroup2… RiskGroup… main Risk… down 2
#> 7 Otu_262 Dorea RiskGroup2… RiskGroup… main Risk… up 3
#> 8 Otu_262 Dorea RiskGroup2… RiskGroup… main Risk… down 3
#> 9 Otu_298 Intes… RiskGroup2… RiskGroup… main Risk… up 2
#> 10 Otu_332 Caten… RiskGroup2… RiskGroup… main Risk… up 3
#> # ℹ 16 more rows
#> # ℹ 1 more variable: methods <chr>