ps_NP: Nasopharyngeal (NP) microbiota data of young infants.

In wsteenhu/microbiomer: Package Containing Utility-functions to Work with Microbiota-data

Description

A dataset containing the nasopharyngeal microbiota data of 97 infants at the age of 1 week, 1 month and 1 year (n = 287 samples). Data from these subjects was already published (Bosch et al, Am J Resp Crit Care Med, 2017), yet for the current data, we revisited our initial bioinformatic processing steps, this time running DADA2 and decontam to curate data.

Usage

ps_NP

Format

A phyloseq-object with 1793 taxa, 287 samples and 5 clinical variables. Datasets contained in this object can be accessed through functions in the phyloseq-package (e.g. otu_table, tax_table, and sample_data). Alternatively, wrappers around these functions contained in this package can be used (e.g. meta_to_df).

seq_id

subject identifier

visit_name

name of the visit, week 1 (w1), month 1 (m1) or year 1 (y1)

age

age in days after birth

birth mode

either vaginal (vag) or by caesarian section (sc)

bf_group_3m_yn

exclusive breastfeeding within the first 3 months of life yes (1) or no (0)

Source

https://www.atsjournals.org/doi/full/10.1164/rccm.201703-0554OC

Examples

ps_NP
ps_NP %>% meta_to_df() %>% dplyr::count(visit_name, birth_mode)

wsteenhu/microbiomer documentation built on March 11, 2021, 6:05 p.m.