throat.meta {MiRKAT}

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