vaginal_meta: Sample metadata of two public vaginal studies

In biobakery/MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

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)

biobakery/MMUPHin documentation built on March 30, 2024, 4:50 a.m.