Help needed: Removing cross-contaminated genera from microtable-class Object

[JayalalKJ]

Hi,

I have encountered an issue with cross-contamination during DNA sequencing. Specifically, I identified two genera, genus1__Otu00003 and genus2__Otu00005 (note that I just pasted out the genus column with the Otu column, which resulted in genus1__Otu00003 and genus2__Otu00005), that appeared in my negative control. I want to remove these contaminated taxa from my micro table object and continue downstream analysis.

[ChiLiubio]

Hi. You can manipulate the tax_table as you want. It should be something like this.

tmp <- dataset$tax_table
tmp <- tmp[tmp$Genus != "genus1__Otu00003", ]
dataset$tax_table <- tmp
dataset$tidy_dataset()