Removing samples from phyloseq otu_table

Question

[zrf1]

I am trying to remove samples from my otu_table in a phyloseq object ps . This is so I can match the samples in my sample_data (which does not have the samples stated below as I removed them due to NAs). I'm using this:

enter code hereto_remove <- c("Sample1", "Sample5", "Sample10", "Sample30")
# using z first to see if it works 
z <- prune_samples(ps@otu_table, !(sample_names() %in% to_remove))

but get this error:

# Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘prune_samples’ for signature ‘"otu_table", "logical"’

How do I go about removing samples from my otu_table?

Answer 1

[antonioggsousa]

Hi,

You're doing a couple of things wrong. First, prune_samples(samples, x) takes 2 positional arguments, samples and x:

• samples: character of samples to keep or logical, where TRUE, is the samples that you want to keep;

• x: phyloseq-class object.

Therefore, what you're doing wrong:

1. you're giving the arguments in the wrong order, and unless you specific the parameters name, that will never work;

2. you're giving a otu-class object and not a phyloseq class object. Here is important to give a phyloseq-class object, because when you remove samples, it is important to remove these samples not only from the otu table but also from metadata/sample data table - this can only work if you give the phyloseq-class object;

3. sample_names() takes one argument, a phyloseq-class object, you did not give any, so does not work.

To fix and solve all these problems, try the following:

to_remove <- c("Sample1", "Sample5", "Sample10", "Sample30")

z <- prune_samples(!(sample_names(ps) %in% to_remove), ps)

This should work. Assuming that ps is your phyloseq-class object.

I hope this answers your question,

António

[zrf1]

My bad, didn't notice that i entered the arguments in the wrong order. Also should put in the phyloseq object for sample_names(). Thank you!