• Calculate DII Polyphenol Subclasses
• SCRIPT
  • Filter in relevant DII subclass polyphenols
  • SUM subclass intake
  • Export Polyphenol Subclass Intakes for DII Calculation

Calculate DII Polyphenol Subclasses

This script takes your data that has been mapped to FooDB polyphenol content, extracts compounds categorized under the six required DII subclasses (flavan-3-ols, Flavones, Flavonols, Flavonones, Anthocyanidins, Isoflavones), and calculates the total intake of these subclasses per participant recall.

INPUTS

• Recall_FooDB_polyphenol_content.csv.bz2: Disaggregated dietary data, mapped to FooDB polyphenol content, at the compound-level
• FooDB_DII_polyphenol_list.csv - Polyphenols under the six polyphenol subclasses required for DII-2014, Provided File

OUTPUTS

• Recall_DII_subclass_by_recall.csv: Sum DII polyphenol subclass content for each participant recall

SCRIPT

Load packages

suppressMessages(library(dplyr))
suppressMessages(library(vroom))
suppressMessages(library(tidyr))
suppressMessages(library(stringr))

Load data

# Load provided file paths
source("provided_files.R")

# Load dietary data mapped to polyphenol content
input_polyphenol_content = vroom::vroom('outputs/Recall_FooDB_polyphenol_content.csv.bz2',
                                        show_col_types = FALSE)

# Eugenol Content in FooDB
# Note: Eugenol doesn't have retention factors from Phenol Explorer
subclasses = vroom::vroom(FooDB_DII_subclasses, show_col_types = FALSE)

Filter in relevant DII subclass polyphenols

input_polyphenol_content_filtered = input_polyphenol_content %>%
  filter(compound_public_id %in% subclasses$compound_public_id) %>%
  # Merge the class information so subclasses are grouped correctly
  left_join(subclasses)

## Joining with `by = join_by(compound_public_id, compound_name)`

SUM subclass intake

The column component contains the DII category.

subclass_intakes = input_polyphenol_content_filtered %>%
  group_by(subject, RecallNo, component) %>%
  # Sum polyphenol category intake, mg by recall
  mutate(component_sum = sum(pp_consumed)) %>%
  ungroup() %>%
  # Keep distinct entries
  distinct(subject, RecallNo, component, .keep_all = TRUE) %>%
  # Minimize the number of columns for pivoting to wide format
  select(c(subject, RecallNo, component, component_sum)) %>%
  # pivot to wide version
  pivot_wider(names_from = component, values_from = component_sum) %>%
  # Rename the columns to match the DII category names in the DietaryIndex function
  rename(
    ISOFLAVONES = Isoflavones,
    "FLA3OL" = "Flavan-3-ols",
    "FLAVONES" = "Flavones",
    "FLAVONOLS" =  "Flavonols",
    "FLAVONONES" = "Flavanones",
    "ANTHOC" = "Anthocyanidins")

Export Polyphenol Subclass Intakes for DII Calculation

vroom::vroom_write(subclass_intakes, 'outputs/Recall_DII_subclass_by_recall.csv', delim = ",")