Metahit Data

73 Indevidual 30 healthy and 43 with disease: 33 with Ulcerative colitis and 10 with Chron disease

Construct phyloseq from kraken

Reading the bracken taxonomy report

## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 3273 taxa and 73 samples ]
## sample_data() Sample Data:       [ 73 samples by 15 sample variables ]
## tax_table()   Taxonomy Table:    [ 3273 taxa by 8 taxonomic ranks ]
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    1992    2255    2378    2360    2452    2665 
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##     969    1457    1703    1644    1822    2043

Filter and Subseting our data

filter step:

- remove human reads
- discard very rare taxa: sum over all samples is at least 100
- realtive abundance in at least one sample is above 0.0001 (0.01%) e.g. 100 reads out of 10^6
- "Core": 0
## phyloseq-class experiment-level object
## otu_table()   OTU Table:         [ 292 taxa and 73 samples ]
## sample_data() Sample Data:       [ 73 samples by 15 sample variables ]
## tax_table()   Taxonomy Table:    [ 292 taxa by 8 taxonomic ranks ]
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   229.0   265.0   274.0   271.2   281.0   291.0 
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   196.0   224.0   241.0   239.3   254.0   288.0

NMDS plots