README.md

In waldronlab/HMP16SData: 16S rRNA Sequencing Data from the Human Microbiome Project

HMP16SData

HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub.

HMP16SData can be installed using BiocManager as follows.

BiocManager::install("HMP16SData")

Once installed, HMP16SData provides two functions to access data – one for variable region 1–3 and another for variable region 3–5. When called, as follows, the functions will download data from an ExperimentHub Amazon S3 (Simple Storage Service) bucket over https or load data from a local cache.

V13()

## class: SummarizedExperiment 
## dim: 43140 2898 
## metadata(2): experimentData phylogeneticTree
## assays(1): 16SrRNA
## rownames(43140): OTU_97.1 OTU_97.10 ... OTU_97.9997 OTU_97.9999
## rowData names(7): CONSENSUS_LINEAGE SUPERKINGDOM ... FAMILY GENUS
## colnames(2898): 700013549 700014386 ... 700114963 700114965
## colData names(7): RSID VISITNO ... HMP_BODY_SUBSITE SRS_SAMPLE_ID

V35()

## class: SummarizedExperiment 
## dim: 45383 4743 
## metadata(2): experimentData phylogeneticTree
## assays(1): 16SrRNA
## rownames(45383): OTU_97.1 OTU_97.10 ... OTU_97.9998 OTU_97.9999
## rowData names(7): CONSENSUS_LINEAGE SUPERKINGDOM ... FAMILY GENUS
## colnames(4743): 700013549 700014386 ... 700114717 700114750
## colData names(7): RSID VISITNO ... HMP_BODY_SUBSITE SRS_SAMPLE_ID

The two data sets are represented as SummarizedExperiment objects, a standard Bioconductor class that is amenable to subsetting and analysis. To maintain brevity, details of the SummarizedExperiment class are not outlined here but the SummarizedExperiment package provides an excellent vignette.

For a complete explanation of the features of HMP16SData, see the package vignette or read the American Journal of Epidemiology article.

Schiffer, L. et al. HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor. Am. J. Epidemiol. (2019).

Griffith, J. C. & Morgan, X. C. Invited Commentary: Improving accessibility of the Human Microbiome Project data through integration with R/Bioconductor. Am. J. Epidemiol. (2019).

Waldron, L. et al. Improving Accessibility of the Human Microbiome Project Data Through Integration With R/Bioconductor. Am. J. Epidemiol. (2019).

waldronlab/HMP16SData documentation built on Nov. 4, 2024, 7:50 a.m.