lungreplicate: Oral and lung microbiome replicate samples data

In kylebittinger/polyafit: Fit observed data to a multivariate Polya distribution

Oral and lung microbiome replicate samples data

Description

Samples, taxa, and read counts for the Charlson-Bittinger study, "Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts."

Usage

lungreplicate_samples

lungreplicate_reads

Format

lungreplicate_samples is a data frame with 42 rows and 5 variables:

sample_id

unique identifiers for each sample

subject_id

unique identifiers for each study participant, matching those in the publication

sample_type

the type of sample, "Oral wash" or "Bronchoalveolar lavage"

replicate_id

unique identifiers for each replicate sample

study_group

the study group into which the participant was recruited, either "Healthy" or "Lung transplant"

lungreplicate_samples is a data frame with 19,362 rows and 4 variables:

otu_id

unique identifiers for each operational taxonomic unit (OTU)

sample_id

unique identifiers for each sample

reads

number of sequence reads attributed to each OTU in each sample

assignment

the taxonomic assignment of the OTU

Source

https://pubmed.ncbi.nlm.nih.gov/22970118/

References

Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, Bushman FD. Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. PLoS One. 2012;7(9):e42786. doi: 10.1371/journal.pone.0042786. Epub 2012 Sep 6. PMID: 22970118; PMCID: PMC3435383.

kylebittinger/polyafit documentation built on Jan. 11, 2023, 8:53 a.m.