clin

Infants who required mechanical ventilation had tracheal aspirates samples collected at 7, 14, and 21 days of age (+/- 48 hours). Infants who were mechanically ventilated and had at least one tracheal aspirate collected were included in this study. Subjects were required to be enrolled within 7 days of age. Bacterial profiles were determined by broad-range amplification and sequence analysis of 16S rRNA genes

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

clin function

A 74x8 data.frame<dl class="dl-horizontal">
<dt><code>study_id</code></dt><dd>A character vector of study IDs</dd>
<dt><code>weight</code></dt><dd>A numeric vector of infant birth weights (Kg)</dd>
<dt><code>sex</code></dt><dd>A factor; infant sex</dd>
<dt><code>gestational_age</code></dt><dd>A numeric vector of gestational age in weeks</dd>
<dt><code>mom_ethncty</code></dt><dd>A factor; maternal ethnicity</dd>
<dt><code>bpd1</code></dt><dd>A factor; BPD severity</dd>
<dt><code>day</code></dt><dd>A numeric vector; days of life at time of sequencing</dd>
<dt><code>Lib</code></dt><dd>A character vector of sequencing library names</dd>
</dl>

Format

A data set containing the clinical data of the subjects sequenced — clin

A 74x8 data.frame<dl class='dl-horizontal'>
<dt><code>study_id</code></dt><dd>A character vector of study IDs</dd>
<dt><code>weight</code></dt><dd>A numeric vector of infant birth weights (Kg)</dd>
<dt><code>sex</code></dt><dd>A factor; infant sex</dd>
<dt><code>gestational_age</code></dt><dd>A numeric vector of gestational age in weeks</dd>
<dt><code>mom_ethncty</code></dt><dd>A factor; maternal ethnicity</dd>
<dt><code>bpd1</code></dt><dd>A factor; BPD severity</dd>
<dt><code>day</code></dt><dd>A numeric vector; days of life at time of sequencing</dd>
<dt><code>Lib</code></dt><dd>A character vector of sequencing library names</dd>
</dl>

clin: A data set containing the clinical data of the subjects sequenced

Description

Usage

Arguments

Format