GrieneisenTSData: Retrieve GrieneisenTS data

In microbiome/microbiomeDataSets: Experiment Hub based microbiome datasets

Retrieve GrieneisenTS data

Description

Obtain longitudinal gut microbiome data in wild baboons from Grieneisen et al. (2021).

Usage

GrieneisenTSData()

baboongut()

Details

The GrieneisenTS dataset contains 16,234 16S rRNA gene sequencing-based microbiome profiles from 585 baboon samples collected over 14 years to determine the heritability of the gut microbiome on various environmental factors such as diet, age, season. Each baboon had an average of 28 samples collected over 4.5 years. The data set can be used to investigate significance of longitudinal sampling at large sample sizes.

This data set contains the 613 most prevalent taxa with a phylogenetic tree.

Column metadata includes the following fields:

sample

Sample ID (character)

baboon_id

Baboon ID (factor)

collection_date

Sample collection date (date; YYYY-MM-DD)

sex

Sex (factor; F/M)

age

Age (numeric)

social_group

Social group ID (factor)

group_size

Social group size (integer)

rain_month_mm

Rain per month(mm) (numeric)

season

Season (factor; dry/wet)

hydro_year

Hydro year (integer)

month

Month (integer)

readcount

Read count (numeric)

plate

Plate (factor)

post_pcr_dna_ng

Post PCR DNA(ng) (numeric)

diet_PC1

Diet Principal coordinate 1 (numeric)

diet_PC2

Diet Principal coordinate 2 (numeric)

diet_PC3

Diet Principal coordinate 3 (numeric)

diet_PC4

Diet Principal coordinate 4 (numeric)

diet_PC5

Diet Principal coordinate 5 (numeric)

diet_PC6

Diet Principal coordinate 6 (numeric)

diet_PC7

Diet Principal coordinate 7 (numeric)

diet_PC8

Diet Principal coordinate 8 (numeric)

diet_PC9

Diet Principal coordinate 9 (numeric)

diet_PC10

Diet Principal coordinate 10 (numeric)

diet_PC11

Diet Principal coordinate 11 (numeric)

diet_PC12

Diet Principal coordinate 12 (numeric)

diet_PC13

Diet Principal coordinate 13 (numeric)

diet_shannon_h

Dietary Shannon's H index (numeric)

asv_richness

Amplicon sequence variant (ASV) richness (integer)

asv_shannon_h

ASV Shannon's H index (numeric)

pc1_bc

Principal coordinate 1 Bray-Curtis dissimilarity (numeric)

pc2_bc

Principal coordinate 2 Bray-Curtis dissimilarity (numeric)

pc3_bc

Principal coordinate 3 Bray-Curtis dissimilarity (numeric)

pc4_bc

Principal coordinate 4 Bray-Curtis dissimilarity (numeric)

pc5_bc

Principal coordinate 5 Bray-Curtis dissimilarity (numeric)

Row metadata of the microbiome data contains taxonomic information on the Domain, Phylum, Class, Order, Family, Genus, and ASV levels.

The row tree consists of a phylogenetic tree build using sequence information of 613 taxa.

As reference sequences the ASV are provided.

Value

A TreeSummarizedExperiment object.

Author(s)

Yagmur Simsek and Leo Lahti

References

Grieneisen et al. (2021): Gut microbiome heritability is nearly universal but environmentally contingent Science 373:6551 https://science.sciencemag.org/content/373/6551/181.full

Examples

tse <- GrieneisenTSData()

microbiome/microbiomeDataSets documentation built on Sept. 25, 2024, 11:42 p.m.