Question: Aggregate By Taxonomy Error
0
2.9 years ago by
nhuda60
nhuda60 wrote:

Hey,

I am getting trouble with aggregating my data. Please suggest me how to aggregate the data by a level say for example "genus". Please see the command and error message below.

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Command

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> MSOTrimG = aggTax(MSO, lvl="genus", out = "MRexperiment")

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Error message

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Error in [.data.frame(fData(obj), , lvl) : undefined columns selected

Regards,

Nazmul

metagenomeseq • 345 views
modified 2.9 years ago by Joseph Nathaniel Paulson270 • written 2.9 years ago by nhuda60
0
2.9 years ago by
United States
Joseph Nathaniel Paulson270 wrote:

Hi Nazmul,

What are the column names of the featureData slot?

colnames(fData(MSO))

You need to use one of those names, or alternatively a vector of your choosing of size nrow(MSO).