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

data(ibd_metadata)

Format

An object of class data.frame with 155 rows and 8 columns.

Value

Sample x metadata dataframe of size 155 x 8

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.

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)
#> SRA_metagenome_name Age Diagnosis Fecal.Calprotectin antibiotic #> G35127 : 1 Min. : 1.00 CD :68 Min. : 1.00 No :134 #> G35128 : 1 1st Qu.: 9.00 Control:34 1st Qu.:20.00 Yes : 18 #> G35152 : 1 Median :16.00 UC :53 Median :36.00 NA's: 3 #> G36347 : 1 Mean :21.66 Mean :36.51 #> G36348 : 1 3rd Qu.:36.00 3rd Qu.:55.00 #> G36349 : 1 Max. :55.00 Max. :73.00 #> (Other):149 NA's :62 #> immunosuppressant mesalamine steroids #> No :100 No :109 No :122 #> Yes: 55 Yes : 44 Yes : 31 #> NA's: 2 NA's: 2 #> #> #> #>