ibd_metadata: Metadata for the PRISM cohort

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

Metadata for the PRISM cohort

Description

Metadata include SRA identifier, age, diagnosis, fecal calprotectin, antibiotic and immunosuppressant usage as well as treatment with mesalamine or steroids.

Usage

data(ibd_metadata)

Format

An object of class data.frame with 155 rows and 8 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). CD/UC vs healthy status is stored in 'Diagnosis'. The order of samples matches those of ibd_taxa.

Value

Sample x metadata dataframe of size 155 x 8

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_metadata)
# convert to numeric
ibd_metadata$Fecal.Calprotectin=as.numeric(ibd_metadata$Fecal.Calprotectin)
ibd_metadata$Age=as.numeric(ibd_metadata$Age)
summary(ibd_metadata)

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