POSTmData: Example Dataset For Illustration

In POSTm: Phylogeny-Guided OTU-Specific Association Test for Microbiome Data

Example Dataset For Illustration

Description

This data set is provided for the purposes of illustrating the use of the software. It was adapted from the vaginal microbiome dataset from Subramaniam et al. (2016). The original dataset consists of 39 individuals with 19 bacterial vaginosis (BV) patients and 20 healthy controls. The sequencing data and metadata are publicly available at NCBI SRA database (PRJNA600021). Initial data processing, lead to 2711 OTUs formed at 97% sequence similarity. FastTree (Price et al, 2010) was used to construct the phylogenetic tree. The OTUs data have been filitered to exclude those with abundance < 0.005% and prevalence < 10%.

Usage

data(POSTmData)

Format

POSTmData contains 4 objects.

metadata

a data.frame containing 30 participants. The data.frame contains 3 columns

SampleID

Character. Unique participant identifiers.

mRace

A dichotomous covariate describing the maternity race.

GC

Gestational complication indicator. "BV" indicates that individual was diagnosed with bacterial vaginosis; "Normal" otherwise

otu

a 39 x 189 matrix containing OTU count data

otutree

a phylogenetic tree constructed using all 2711 OTU sequences

otuseq

a character vector of OTU sequencing data used to construct the phylogenetic tree

POSTm documentation built on May 29, 2024, 9:24 a.m.