Ruminotypes: Whole Ruminotypes dataset communities

In lauzingaretti/LinkHD-examples: LinkHD: a versatile framework to explore and integrate heterogeneous data

Description

Ruminotypes dataset contains communities (16_S, 18_S and Archaea) measuares from 65 loose-housed lactating Holstein cows. The study aims evaluating the relationships between communities and methane emmision yield

Format

A list with seven components:

16_S

matrix with 61 rows and 1198 columns. Each row represents a sample and each column represent one normalized OTU.

Archea

a matrix with 61 rows (samples) and 453 normalized columns (Archea IDs).

18_S

a matrix with 61 rows and 107 normalized columns (protozoa level).

phenotype

data frame with 61 rows and 5 columns representing methane emission levels with a set of corrections.

Taxa_16S

a matrix with 1198 rows and 9 columns indicating the Taxa information for 16_S OTU.

Taxa_18S

a matrix with 112 rows and 18 columns indicating the Taxa information for 18_S samples.

Taxa_Archea

a matrix with 453 rows and 7 columns indicating the Taxa information for archea samples.

References

Ramayo-Caldas Y, Zingaretti LM, Bernard A, Estellé J, Popova M, Pons N, Bellot P, Mach N, Rau A, Roume H, Pérez-Enciso M, Faverdin N, Edouard N, Dusko S, Morgavi DP, Renand G. Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows In press.

Examples

data(Ruminotypes)

lauzingaretti/LinkHD-examples documentation built on Dec. 21, 2021, 9:42 a.m.