Metadata for the PRISM cohort

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  
#>                                         
#>                                         
#>                                         
#>