Extra Recipes Steps for Dealing with Omics Data.

scimo

scimo provides extra recipes steps for dealing with omics data, while also being adaptable to other data types.

Installation

You can install scimo from GitHub with:

# install.packages("remotes")
remotes::install_github("abichat/scimo")

Example

The cheese_abundance dataset describes fungal community abundance of 74 Amplicon Sequences Variants (ASVs) sampled from the surface of three different French cheeses.

library(scimo)
data("cheese_abundance", "cheese_taxonomy")

cheese_abundance
#> # A tibble: 9 × 77
#>   sample    cheese    rind_type asv_01 asv_02 asv_03 asv_04 asv_05 asv_06 asv_07
#>   <chr>     <chr>     <chr>      <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>
#> 1 sample1-1 Saint-Ne… Natural        1      0     38     40      1      2     31
#> 2 sample1-2 Saint-Ne… Natural        3      4     38     61      4      4     48
#> 3 sample1-3 Saint-Ne… Natural       28     16     33     23     31     29     21
#> 4 sample2-1 Livarot   Washed         0      2      1      0      5      1      0
#> 5 sample2-2 Livarot   Washed         0      0      4      0      1      1      2
#> 6 sample2-3 Livarot   Washed         0      1      2      0      2      1      0
#> 7 sample3-1 Epoisses  Washed         4      2      3      0      2      5      0
#> 8 sample3-2 Epoisses  Washed         0      0      0      0      0      0      0
#> 9 sample3-3 Epoisses  Washed         0      0      1      0      0      0      2
#> # ℹ 67 more variables: asv_08 <dbl>, asv_09 <dbl>, asv_10 <dbl>, asv_11 <dbl>,
#> #   asv_12 <dbl>, asv_13 <dbl>, asv_14 <dbl>, asv_15 <dbl>, asv_16 <dbl>,
#> #   asv_17 <dbl>, asv_18 <dbl>, asv_19 <dbl>, asv_20 <dbl>, asv_21 <dbl>,
#> #   asv_22 <dbl>, asv_23 <dbl>, asv_24 <dbl>, asv_25 <dbl>, asv_26 <dbl>,
#> #   asv_27 <dbl>, asv_28 <dbl>, asv_29 <dbl>, asv_30 <dbl>, asv_31 <dbl>,
#> #   asv_32 <dbl>, asv_33 <dbl>, asv_34 <dbl>, asv_35 <dbl>, asv_36 <dbl>,
#> #   asv_37 <dbl>, asv_38 <dbl>, asv_39 <dbl>, asv_40 <dbl>, asv_41 <dbl>, …

glimpse(cheese_taxonomy)
#> Rows: 74
#> Columns: 9
#> $ asv     <chr> "asv_01", "asv_02", "asv_03", "asv_04", "asv_05", "asv_06", "a…
#> $ lineage <chr> "k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Dothideales|f__D…
#> $ kingdom <chr> "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi",…
#> $ phylum  <chr> "Ascomycota", "Ascomycota", "Ascomycota", "Ascomycota", "Ascom…
#> $ class   <chr> "Dothideomycetes", "Eurotiomycetes", "Eurotiomycetes", "Euroti…
#> $ order   <chr> "Dothideales", "Eurotiales", "Eurotiales", "Eurotiales", "Euro…
#> $ family  <chr> "Dothioraceae", "Aspergillaceae", "Aspergillaceae", "Aspergill…
#> $ genus   <chr> "Aureobasidium", "Aspergillus", "Penicillium", "Penicillium", …
#> $ species <chr> "Aureobasidium Group pullulans", "Aspergillus fumigatus", "Pen…

list_family <- split(cheese_taxonomy$asv, cheese_taxonomy$family)
head(list_family, 2)
#> $Aspergillaceae
#> [1] "asv_02" "asv_03" "asv_04" "asv_05" "asv_06" "asv_07" "asv_08" "asv_09"
#> 
#> $Debaryomycetaceae
#>  [1] "asv_10" "asv_11" "asv_12" "asv_13" "asv_14" "asv_15" "asv_16" "asv_17"
#>  [9] "asv_18" "asv_19" "asv_20" "asv_21" "asv_22"

The following recipe will

1. aggregate the ASV variables at the family level, as defined by list_family;
2. transform counts into proportions;
3. discard variables those p-values are above 0.05 with a Kruskal-Wallis test against cheese.

rec <-
  recipe(cheese ~ ., data = cheese_abundance) %>% 
  step_aggregate_list(all_numeric_predictors(),
                      list_agg = list_family, fun_agg = sum) %>%
  step_rownormalize_tss(all_numeric_predictors()) %>% 
  step_select_kruskal(all_numeric_predictors(), 
                      outcome = "cheese", cutoff = 0.05) %>%
  prep()

rec
#> 
#> ── Recipe ──────────────────────────────────────────────────────────────────────
#> 
#> ── Inputs
#> Number of variables by role
#> outcome:    1
#> predictor: 76
#> 
#> ── Training information
#> Training data contained 9 data points and no incomplete rows.
#> 
#> ── Operations
#> • Aggregation of: asv_01, asv_02, asv_03, asv_04, asv_05, ... | Trained
#> • TSS normalization on: Aspergillaceae and Debaryomycetaceae, ... | Trained
#> • Kruskal filtering against cheese on: Aspergillaceae, ... | Trained

bake(rec, new_data = NULL)
#> # A tibble: 9 × 8
#>   sample    rind_type cheese  Debaryomycetaceae Dipodascaceae Saccharomycetaceae
#>   <fct>     <fct>     <fct>               <dbl>         <dbl>              <dbl>
#> 1 sample1-1 Natural   Saint-…            0.719         0.0684           0.113   
#> 2 sample1-2 Natural   Saint-…            0.715         0.0725           0.119   
#> 3 sample1-3 Natural   Saint-…            0.547         0.277            0.0938  
#> 4 sample2-1 Washed    Livarot            0.153         0.845            0.000854
#> 5 sample2-2 Washed    Livarot            0.150         0.848            0.00106 
#> 6 sample2-3 Washed    Livarot            0.160         0.837            0.00108 
#> 7 sample3-1 Washed    Epoiss…            0.0513        0.944            0.00327 
#> 8 sample3-2 Washed    Epoiss…            0.0558        0.941            0.00321 
#> 9 sample3-3 Washed    Epoiss…            0.0547        0.942            0.00329 
#> # ℹ 2 more variables: `Saccharomycetales fam Incertae sedis` <dbl>,
#> #   Trichosporonaceae <dbl>

To see which variables are kept and the associated p-values, you can use the tidy method on the third step:

tidy(rec, 3)
#> # A tibble: 13 × 4
#>    terms                                    pv kept  id                  
#>    <chr>                                 <dbl> <lgl> <chr>               
#>  1 Aspergillaceae                       0.0608 FALSE select_kruskal_WKayj
#>  2 Debaryomycetaceae                    0.0273 TRUE  select_kruskal_WKayj
#>  3 Dipodascaceae                        0.0273 TRUE  select_kruskal_WKayj
#>  4 Dothioraceae                         0.101  FALSE select_kruskal_WKayj
#>  5 Lichtheimiaceae                      0.276  FALSE select_kruskal_WKayj
#>  6 Metschnikowiaceae                    0.0509 FALSE select_kruskal_WKayj
#>  7 Mucoraceae                           0.0608 FALSE select_kruskal_WKayj
#>  8 Phaffomycetaceae                     0.0794 FALSE select_kruskal_WKayj
#>  9 Saccharomycetaceae                   0.0273 TRUE  select_kruskal_WKayj
#> 10 Saccharomycetales fam Incertae sedis 0.0221 TRUE  select_kruskal_WKayj
#> 11 Trichomonascaceae                    0.0625 FALSE select_kruskal_WKayj
#> 12 Trichosporonaceae                    0.0273 TRUE  select_kruskal_WKayj
#> 13 Wickerhamomyceteae                   0.177  FALSE select_kruskal_WKayj

Notes

protection stack overflow error

If you have a very large dataset, you may encounter this error:

data("pedcan_expression")
recipe(disease ~ ., data = pedcan_expression) %>% 
    step_select_cv(all_numeric_predictors(), prop_kept = 0.1) 
#> Error: protect(): protection stack overflow

It is linked to how R handles many variables in formulas. To solve it, pass only the dataset to recipe() and manually update roles with update_role(), like in the example below:

recipe(pedcan_expression) %>% 
  update_role(disease, new_role = "outcome") %>% 
  update_role(-disease, new_role = "predictor") %>% 
  step_select_cv(all_numeric_predictors(), prop_kept = 0.1) 
#> 
#> ── Recipe ──────────────────────────────────────────────────────────────────────
#> 
#> ── Inputs
#> Number of variables by role
#> outcome:       1
#> predictor: 19196
#> 
#> ── Operations
#> • Top CV filtering on: all_numeric_predictors()

Steps for variable selection

Like colino, scimo proposes 3 arguments for variable selection steps based on a statistic: n_kept, prop_kept and cutoff.

• n_kept and prop_kept deal with how many variables will be kept in the preprocessed dataset, based on an exact count of variables or a proportion relative to the original dataset. They are mutually exclusive.

• cutoff removes variables whose statistic is below (or above, depending on the step) it. It could be used alone or in addition to the two others.

Dependencies

scimo doesn’t introduce any additional dependencies compared to recipes.