vaginal_abd: Species level feature abundance data of two public vaginal...

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

Species level feature abundance data of two public vaginal studies

Description

Species level relative abundance profiles of vaginal samples in the two public studies provided in curatedMetagenomicData.

Usage

data(vaginal_abd)

Format

A feature-by-sample matrix of species-level profiles

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_abd)
# features included
rownames(vaginal_abd)
# These are relative abundances
apply(vaginal_abd, 2, sum)
# 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_abd <- otu_table(physeq)@.Data

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