MicrobiomeBenchmarkDataAnalyses

library(MicrobiomeBenchmarkDataAnalyses)
library(dplyr)

Some overall numbers to cite in the Results

For the statement:

We utilized Human Microbiome Project (HMP1) data (Human Microbiome Project Consortium, 2012) comprising both 16S rRNA (V13 and V15 variable region datasets, each 311 measurements on 132 participants)

V13:

data('sampleMetadata', package = 'MicrobiomeBenchmarkData')
filter(sampleMetadata, dataset ==  "HMP_2012_16S_gingival_V13") |>
    nrow()

## [1] 311

filter(sampleMetadata, dataset ==  "HMP_2012_16S_gingival_V13") |>
    pull(subject_id) |>
    unique() |>
    length()

## [1] 132

V35:

filter(sampleMetadata, dataset ==  "HMP_2012_16S_gingival_V35") |>
    nrow()

## [1] 311

filter(sampleMetadata, dataset ==  "HMP_2012_16S_gingival_V35") |>
    pull(subject_id) |>
    unique() |>
    length()

## [1] 132

… and shotgun metagenomic sequencing (MGX, 16 measurements on 5 participants)

filter(sampleMetadata, dataset == "HMP_2012_WMS_gingival") |>
    nrow()

## [1] 16

filter(sampleMetadata, dataset == "HMP_2012_WMS_gingival") |>
  pull(subject_id) |>
  unique() |>
  length()

## [1] 5