vaginal_abd {MMUPHin} | R Documentation |
Species level relative abundance profiles of vaginal samples in
the two public studies provided in
curatedMetagenomicData
.
data(vaginal_abd)
A feature-by-sample matrix
of species-level profiles
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.
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