throat.meta: Simulated metadata for microbiome regression-based analysis
In MiRKAT: Microbiome Regression-Based Kernel Association Tests

throat.meta

R Documentation

Simulated metadata for microbiome regression-based analysis

Description

Simulation code can be seen in ?KRV Corresponding OTU matrix is stored in "throat.otu.tab"

Usage

data(throat.meta)

Format

A data frame with 59 rows and 16 columns, rows being participants and columns being different covariates to possibly be accounted for in any utilized linear models.

throat.meta is part of a microbiome data set for studying the effect of smoking on the upper respiratory tract microbiome. This data set comes from the throat microbiome of left body side. It contains 60 subjects consisting of 32 nonsmokers and 28 smokers.

BarcodeSequence: Sequence of DNA that allows for the identification of the specific species of bacteria. See GUniFrac for more details
LinkerPrimerSequence: Sequence of DNA that aids in locating the Barcode Sequence. See GUniFrac for more details
SmokingStatus: whether or not each patient is a "Smoker" or a "NonSmoker"
PatientID: Identifying integer label given to each patient
SampleIndex: Labels each patient as being from this particular sample, so as possibly be able to use multiple samples at once
AirwaySite: Part of body where our samples were taken from from in each participant
SideOfBody: Which side of the body the samples were taken from
SampleType: What kind of sample each one is; should all be patientsamples
RespiratoryDiseaseStatus_severity_timeframe: Whether or not the patient has had a respiratory disease, and if so which one_severity of said disease_whether or not that disease is still active. If there has been no such disease in the patient's medical history, the patient's value is "healthy" in this column
AntibioticUsePast3Months_TimeFromAntibioticUsage: Whether or not the patient has used antibiotics in the past month_if so, how long ago it was. If not antibiotics have been used in the past month, the patient's value is "None" in this column
Age: Age of the patient
Sex: The sex of the patient
PackYears: Unit of measurement measuring the intensity of smoking; average number of packs per day times the number of years the patient has been smoking. If patient has never smoked, their value is 0 for this column
TimeFromLastCig: Minutes since the patient's last cigarette
TimeFromLastMeal: Minutes since the patient's last meal
Description: See Charleston paper and other sources