ibd_functions: Functions from the PRISM cohort

In hallucigenia-sparsa/seqgroup: Analysis of Sequencing Data with Groups

Functions from the PRISM cohort

Description

Function (i.e. enzyme-coding gene) abundances extracted from whole-genome shotgun data of stool samples.

Usage

data(ibd_functions)

Format

An object of class data.frame with 2113 rows and 155 columns.

Details

Stool samples were taken from patients with Crohn's disease (CD, n=68) and ulcerative colitis (UC, n=53) as well as healthy controls (n=34). The order of samples matches those of ibd_taxa. Functional assignment was carried out with the HUMAnN2 pipeline. Enzyme names as well as EC numbers are given.

Value

Function x sample matrix of size 2113 x 155

References

Franzosa et al. (2019) Gut microbiome structure and metabolic activity in inflammatory bowel disease Nature Microbiology 4, 293-305 Nature Microbiology

Examples

data(ibd_functions)

hallucigenia-sparsa/seqgroup documentation built on July 6, 2022, 1:11 p.m.