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nhanhocu / metamicrobiomeR

An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studies using random effects models
https://github.com/nhanhocu/metamicrobiomeR
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remove rare taxa from count table #21

Open sumitra20 opened 1 year ago

sumitra20 commented 1 year ago

Hi,

I have a tax abundance count table and i would like to remove rare taxa and i want to set a minimum number of samples a taxa must be observed. If a taxa does not present in more than 3 samples i would like to remove them. Will that be possible with this?

                                R13P1_R R13P6_R R13P2_R R13P3_R R13P5_R R22P2_R
Acidobacteria                     11397   11225   12410   20227    8862    5310
candidate division NC10               0       0       0       0       0       0
Candidatus Aminicenantes              0       0    1205      47       0       0
Candidatus Dadabacteria               0       0       3       0       2       0
Candidatus Eisenbacteria              1000    20      0      1468    10      0
Candidatus Rokubacteria               0       0     134       0       0     510