Version of make_biom that allows a change in matrix_element_type

make_biom.R

make_biom2<-function (data, sample_metadata = NULL, observation_metadata = NULL, 
    id = NULL,matrix_element_type="int") 
{
    if (!is.null(observation_metadata)) {
        rows = mapply(list, SIMPLIFY = FALSE, id = as.list(rownames(data)), 
            metadata = alply(as.matrix(observation_metadata), 
                1, .expand = FALSE, .dims = TRUE))
    }
    else {
        rows = mapply(list, id = as.list(rownames(data)), metadata = NA, 
            SIMPLIFY = FALSE)
    }
    if (!is.null(sample_metadata)) {
        columns = mapply(list, SIMPLIFY = FALSE, id = as.list(colnames(data)), 
            metadata = alply(as.matrix(sample_metadata), 1, .expand = FALSE, 
                .dims = TRUE))
    }
    else {
        columns = mapply(list, id = as.list(colnames(data)), 
            metadata = NA, SIMPLIFY = FALSE)
    }
    datalist = as.list(as.data.frame(as(t(data), "matrix")))
    names(datalist) <- NULL
    format_url = "http://biom-format.org/documentation/format_versions/biom-1.0.html"
    return(biom(list(id = id, format = "Biological Observation Matrix 1.0.0-dev", 
        format_url = format_url, type = "OTU table", generated_by = sprintf("biom %s", 
            packageVersion("biom")), date = as.character(Sys.time()), 
        matrix_type = "dense", matrix_element_type = matrix_element_type, shape = dim(data), 
        rows = rows, columns = columns, data = datalist)))
}