mrsa_clin

Data from a study to define the nasal microbiome of hospital inpatients who are persistently colonized with methicillin-resistant Staphylococcus aureus (MRSA) compared with matched, non-colonized controls. See original paper for matching proceedure.

datasets

A reliable alternative to popular microbiome analysis R packages. We provide standard tools as well as novel extensions on standard analyses to improve interpretability and the analyst<e2><80><99>s ability to communicate results, all while maintaining object malleability to encourage open source collaboration.

Charlie Carpenter

tidyMicro

A Pipeline for Microbiome Analysis and Visualization

Dan Frank

Kayla Williamson

Rachel Johnson

mrsa_clin function

A 52x15 data.frame<dl class="dl-horizontal">
 <dt><code>Lib</code></dt><dd>A character vector of sequencing library names</dd>
 <dt><code>Subject</code></dt><dd>Subject names</dd>
 <dt><code>Age</code></dt><dd>Subject's Ages in years</dd>
 <dt><code>Antibiotics</code></dt><dd>Whether or not subjects were on some form of antibiotics. 'N' = No, 'Y' = Yes</dd>
 <dt><code>Case_or_Control</code></dt><dd>Whether or not the subject was MRSA positive. 'Case' = MRSA positive</dd>
 <dt><code>Decade</code></dt><dd>Subjects age in decades. '8' means the subject was in their 80s</dd>
 <dt><code>Diabetes</code></dt><dd>Whether or not the subject had diabets. 'N' = No, 'Y' = Yes</dd>
 <dt><code>Match</code></dt><dd>Numeric variable indicating matchus subjects</dd>
 <dt><code>MRSA_Postive</code></dt><dd>Whether or not the subject was MRSA positive. 'Y' = MRSA positive</dd>
 <dt><code>Nasal_Steroids</code></dt><dd>Whether or not the subject was using nasal steroids. 'N' = No, 'Y' = Yes</dd>
 <dt><code>Nursing_Home</code></dt><dd>Whether or not the subject was staying in a nursing home. 'N' = No, 'Y' = Yes</dd>
 <dt><code>Smoking</code></dt><dd>Subject's smoking status. 'F' = Former, 'N' = Never, 'Y' = Yes/current smoker</dd><dt><code>Lib names</code></dt><dd>The following columns are the sequencing counts for each library with library names</dd>
</dl>

Format

A data set containing the clinical data of the subjects sequenced for MRSA study — mrsa_clin

A data set containing the clinical data of the subjects sequenced for MRSA study

mrsa_clin: A data set containing the clinical data of the subjects sequenced for MRSA study

Description

Usage

Arguments

Format