Extract data

[TuomasBorman]

Function structure discussed here: #2

The second step is to extract the data from SE. We can develop an internal function that does that for all our methods. We could use this to get idea: https://github.com/microbiome/mia/blob/48e319786b05e541bf87bdb2bff151f9d75dbef9/R/runCCA.R#L448

The internal function could be in this format:

.extract_data <- function(x, formula, features){
    return(long_formatted_table)
}

where x is SummarizedExperiment object. The data is extracted based on formula. features is applicable when LHS of formula specifies assay; it is used for selecting specific rows.

You can add this to utils.R.