This notebook is show how to use Q2-DSFDR in command line interface

convert feature table to qiime2 qza artifact



In [1]:

    
!qiime tools import \
--input-path ../data/deblur-feature-table.biom \
--type 'FeatureTable[Frequency]' \
--source-format BIOMV210Format \
--output-path ../data/dblr_haddad.qza

select interested category to compare using DS-FDR



In [2]:

    
!qiime dsfdr permutation-fdr \
--i-table ../data/dblr_haddad.qza \
--m-metadata-file ../data/metadata_rare2k.txt \
--m-metadata-column 'exposure_type' \
--o-reject haddad.dsfdr --verbose









    



DEBUG:Processing 740 features
DEBUG:92 samples in group1
DEBUG:90 samples in group2
DEBUG:Using statistic meandiff
DEBUG:Rejected 105 features
Saved SampleData[AlphaDiversity] to: haddad.dsfdr.qza

output the list of differential abundant taxa (True indicates statistical significance)



In [7]:

    
!qiime tools export haddad.dsfdr.qza --output-dir haddad.dsfdr.results