R/DA.phyloseq.R

In Russel88/DAtest: Comparing Differential Abundance/Expression Methods

DA.phyloseq <- function(data, predictor, paired = NULL, covars = NULL){
 
  ok <- tryCatch({
    loadNamespace("phyloseq")
    TRUE
  }, error=function(...) FALSE)
  
  if (ok){
    if(length(predictor) > 1 | length(paired) > 1) stop("When data is a phyloseq object predictor and paired should only contain the name of the variables in sample_data")
    if(!predictor %in% phyloseq::sample_variables(data)) stop(paste(predictor,"is not present in sample_data(data)"))
    if(!is.null(paired)){
      if(!paired %in% phyloseq::sample_variables(data)) stop(paste(paired,"is not present in sample_data(data)"))
    }
    count_table <- phyloseq::otu_table(data)
    if(!phyloseq::taxa_are_rows(data)) count_table <- t(count_table)
    predictor <- unlist(phyloseq::sample_data(data)[,predictor])
    if(!is.null(paired)) paired <- suppressWarnings(as.factor(as.matrix(phyloseq::sample_data(data)[,paired])))
    if(!is.null(covars)){
      covars.n <- covars
      covars <- list()
      for(i in 1:length(covars.n)){
        covars[[i]] <- unlist(phyloseq::sample_data(data)[,covars.n[i]])
      }
      names(covars) <- covars.n
    } 
    
    DA.data <- list(count_table = count_table,
                    predictor = predictor,
                    paired = paired,
                    covars = covars)
    
    return(DA.data)
    
  } else {
    stop("phyloseq package required")
  }
  
}