How to extract to columns from a phyloseq sample_data object?

Question

[dpc]

Hi I have converted my data into phyloseq object for statistical analysis. From the sample_data object I want to select two specific columns which I will further combine with a distance matrix. But, I am unable to extract out those two columns. I am using these codes which is reversing the following error:

My code:

sd = as.matrix(sample_data(physeq))
sd = sd %>%
  select("SampleID", "type") %>%
  mutate_if(is.factor,as.character)

Error reversed:

Error in UseMethod("select_") : 
  no applicable method for 'select_' applied to an object of class "c('matrix', 'array', 'character')"

How should I do the step?

Thanks dpc

[cpad0112]

try.

sample_data(physeq) %>%
    data.frame() %>%
    select("SampleID", "type") %>%
    mutate_if(is.factor,as.character)

Answer 1

[antonioggsousa]

Hi,

The problem is that pipes, as far as I know, only works with tibble data frames or data frames. Therefore you should coerce your sample metadata from phyloseq class into a data frame class, by doing:

sd = data.frame(sample_data(physeq))

I hope this solves your problem,

António