struggling in understanding the meaning of a particular line from a script

General
1

Hi friends!!! I am a novice in R. My question may seem silly, but please bear with me. I am trying to understand some codes written with phyloseq package and struggling. Can you please tell me what exactly is meant by the following code and mainly its highlighted portion?
This code actually used to make a heatmap for microbial species relative abundance above a certain threshold limit.

Thanks and regards,

DC7

2

You did not provide any code.

3

oops!!! Out of my mind...

keepTaxa <- ((apply(otu_table(human_data.ra) >= 0.005,1,sum,na.rm=TRUE) > 2) | (apply(otu_table(human_data.ra) >= 0.01, 1, sum,na.rm=TRUE) > 0))

table(keepTaxa)

Thanks,
DC7

4

the key function in that appears to be otu_table so I would start by reading the documentation of phyloseq to understand what that would do. Then the rest is applying cut offs, apply is iteratively over the data and summing sum the results etc.

5

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