vaginal_meta {MMUPHin} | R Documentation

## Sample metadata of two public vaginal studies

### Description

Metadata information of vaginal samples in the two public studies provided in `curatedMetagenomicData`.

### Usage

    data(vaginal_meta)

### Format

A `data.frame` of per-sample metadata information

### Source

`curatedMetagenomicData`

### References

Pasolli, Edoardo, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini et al. "Accessible, curated metagenomic data through ExperimentHub." Nature methods 14, no. 11 (2017): 1023.

### Examples

    data(vaginal_meta)
    # has vaginal samples across two studies
    table(vaginal_meta$studyID, vaginal_meta$body_site)
    # The following were used to generate the object
    # library(curatedMetagenomicData)
    # library(phyloseq)
    # datasets <- curatedMetagenomicData(
    #   "*metaphlan_bugs_list.vagina*",
    #   dryrun = FALSE)
    # Construct phyloseq object from the five datasets
    # physeq <-
      # Aggregate the five studies into ExpressionSet
    #   mergeData(datasets) %>%
      # Convert to phyloseq object
    #   ExpressionSet2phyloseq() %>%
      # Subset features to species
    #   subset_taxa(!is.na(Species) & is.na(Strain)) %>%
      # Normalize abundances to relative abundance scale
    #   transform_sample_counts(function(x) x / sum(x)) %>%
      # Filter features to be of at least 1e-5 relative abundance in two samples
    #   filter_taxa(kOverA(2, 1e-5), prune = TRUE)
    # vaginal_meta <- data.frame(sample_data(physeq))
    # vaginal_meta$studyID <- factor(vaginal_meta$studyID)

[Package MMUPHin version 1.1.0 Index]