diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9693bf4..c2a3d98 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ exclude: |
   (?x)(
       ^assets/|
       ^docs/.*.html|
-      ^data-raw/*.txt|
+      ^inst/extdata|
       ^man/
    )
 repos:
diff --git a/DESCRIPTION b/DESCRIPTION
index 40c34ff..97a201c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -16,9 +16,9 @@ BugReports: https://github.com/CCBR/reneeTools/issues
 Depends:
     R (>= 2.10)
 Imports:
-    assertthat,
     DESeq2,
     dplyr,
+    S7,
     tidyr
 Suggests:
     readr,
diff --git a/NAMESPACE b/NAMESPACE
index 024a199..fedbab0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,7 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(create_deseq_obj)
+export(counts_dat_to_matrix)
 export(filter_low_counts)
-export(read_raw_counts)
+export(meta_tbl_to_dat)
+export(reneeDataSetFromDataFrames)
+export(reneeDataSetFromFiles)
+export(run_deseq2)
+if (getRversion() < "4.3.0") importFrom("S7", "@")
 importFrom(dplyr,"%>%")
diff --git a/NEWS.md b/NEWS.md
index cd5e27e..fc8ce76 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,7 +2,10 @@
 
 - Create a `NEWS.md` file to track changes to the package.
 
-## New functions
+## Main functions & classes
 
+- `reneeDataSet` (#16)
+  - `reneeDataSetFromFiles()` (#16)
+  - `reneeDataSetFromDataFrames()` (#16)
+  - `run_deseq2()` (#16)
 - `filter_low_counts()` (#10)
-- `create_deseq_obj()` (#13)
diff --git a/R/counts.R b/R/counts.R
new file mode 100644
index 0000000..8bb3a9b
--- /dev/null
+++ b/R/counts.R
@@ -0,0 +1,25 @@
+#' Convert a data frame of gene counts to a matrix
+#'
+#' @param counts_tbl expected gene counts from RSEM as a data frame or tibble.
+#'
+#' @return matrix of gene counts with rows as gene IDs
+#' @export
+#'
+#' @examples
+#' counts_dat_to_matrix(head(gene_counts))
+counts_dat_to_matrix <- function(counts_tbl) {
+  gene_id <- GeneName <- NULL
+  counts_dat <- counts_tbl %>%
+    # deseq2 requires integer counts
+    dplyr::mutate(dplyr::across(
+      dplyr::where(is.numeric),
+      \(x) as.integer(round(x, 0))
+    )) %>%
+    as.data.frame()
+  row.names(counts_dat) <- counts_dat %>% dplyr::pull("gene_id")
+  # convert counts tibble to matrix
+  counts_mat <- counts_dat %>%
+    dplyr::select(-c(gene_id, GeneName)) %>%
+    as.matrix()
+  return(counts_mat)
+}
diff --git a/R/deseq2.R b/R/deseq2.R
index c6459e8..5a97575 100644
--- a/R/deseq2.R
+++ b/R/deseq2.R
@@ -1,37 +1,29 @@
-#' Create DESeq2 object from gene counts and sample metadata
+#' Run DESeq2 on a reneeDataSet
 #'
-#' @param counts_tbl expected gene counts from RSEM as a data frame or tibble.
-#' @param meta_dat   sample metadata as a data frame with rownames as sample IDs.
-#' @param design     model formula for experimental design. Columns must exist in `meta_dat`.
+#' @param renee_ds reneeDataSet object
+#' @param design   model formula for experimental design. Columns must exist in `meta_dat`.
+#' @param ...      remaining variables are forwarded to `DESeq2::DESeq()`.
 #'
-#' @return DESeqDataSet
+#' @return reneeDataSet object with DESeq2 slot filled
 #' @export
 #'
 #' @examples
-#' sample_meta <- data.frame(
-#'   row.names = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"),
-#'   condition = factor(c("knockout", "knockout", "wildtype", "wildtype"),
-#'     levels = c("wildtype", "knockout")
+#' rds <- reneeDataSetFromFiles(
+#'   system.file("extdata",
+#'     "RSEM.genes.expected_count.all_samples.txt",
+#'     package = "reneeTools"
+#'   ),
+#'   system.file("extdata", "sample_metadata.tsv",
+#'     package = "reneeTools"
 #'   )
 #' )
-#' dds <- create_deseq_obj(gene_counts, sample_meta, ~condition)
-create_deseq_obj <- function(counts_tbl, meta_dat, design) {
-  gene_id <- GeneName <- NULL
-  counts_dat <- counts_tbl %>%
-    # deseq2 requires integer counts
-    dplyr::mutate(dplyr::across(
-      dplyr::where(is.numeric),
-      \(x) as.integer(round(x, 0))
-    )) %>%
-    as.data.frame()
-  row.names(counts_dat) <- counts_dat %>% dplyr::pull("gene_id")
-  # convert counts tibble to matrix
-  counts_mat <- counts_dat %>%
-    dplyr::select(-c(gene_id, GeneName)) %>%
-    as.matrix()
-
-  # sample IDs must be in the same order
-  assertthat::are_equal(colnames(counts_mat), rownames(meta_dat))
-
-  return(DESeq2::DESeqDataSetFromMatrix(counts_mat, meta_dat, design))
+#' run_deseq2(rds, ~condition)
+run_deseq2 <- function(renee_ds, design, ...) {
+  dds <- DESeq2::DESeqDataSetFromMatrix(
+    renee_ds@counts,
+    renee_ds@sample_meta,
+    design
+  )
+  renee_ds@analyses$deseq2_ds <- DESeq2::DESeq(dds, ...)
+  return(renee_ds)
 }
diff --git a/R/metadata.R b/R/metadata.R
new file mode 100644
index 0000000..730edad
--- /dev/null
+++ b/R/metadata.R
@@ -0,0 +1,22 @@
+#' Convert sample metadata from a tibble to a dataframe with sample IDs as row names
+#'
+#' @param meta_tbl tibble with `sample_id` column
+#'
+#' @return dataframe where row names are the sample IDs
+#' @export
+#'
+#' @examples
+#' sample_meta_tbl <- readr::read_tsv(system.file("extdata",
+#'   "sample_metadata.tsv",
+#'   package = "reneeTools"
+#' ))
+#' head(sample_meta_tbl)
+#' meta_tbl_to_dat(sample_meta_tbl)
+meta_tbl_to_dat <- function(meta_tbl) {
+  sample_id <- NULL
+  meta_dat <- meta_tbl %>%
+    as.data.frame() %>%
+    dplyr::select(-sample_id)
+  rownames(meta_dat) <- meta_tbl %>% dplyr::pull(sample_id)
+  return(meta_dat)
+}
diff --git a/R/renee-class.R b/R/renee-class.R
new file mode 100644
index 0000000..f908a68
--- /dev/null
+++ b/R/renee-class.R
@@ -0,0 +1,64 @@
+reneeDataSet <- S7::new_class("renee",
+  properties = list(
+    counts = S7::new_S3_class("matrix"),
+    sample_meta = S7::class_data.frame,
+    analyses = S7::class_list
+  ),
+  constructor = function(count_matrix, sample_meta_dat) {
+    S7::new_object(S7::S7_object(),
+      counts = count_matrix,
+      sample_meta = sample_meta_dat,
+      analyses = list()
+    )
+  }
+)
+
+#' Construct a reneeDataSet object from tsv files.
+#'
+#' @param gene_counts_filepath path to tsv file of expected gene counts from RSEM.
+#' @param sample_meta_filepath path to tsv file with sample IDs and metadata for differential analysis.
+#'
+#' @return reneeDataSet object
+#' @export
+#'
+#' @examples
+#' reneeDataSetFromFiles(
+#'   system.file("extdata", "RSEM.genes.expected_count.all_samples.txt", package = "reneeTools"),
+#'   system.file("extdata", "sample_metadata.tsv", package = "reneeTools")
+#' )
+reneeDataSetFromFiles <- function(gene_counts_filepath, sample_meta_filepath) {
+  count_dat <- readr::read_tsv(gene_counts_filepath)
+  sample_meta_dat <- readr::read_tsv(sample_meta_filepath)
+  return(reneeDataSetFromDataFrames(count_dat, sample_meta_dat))
+}
+
+#' Construct a reneeDataSet object from data frames
+#'
+#' @param gene_counts_dat expected gene counts from RSEM as a data frame or tibble.
+#'   Must contain a `gene_id` column and a column for each sample ID in the metadata.
+#' @param sample_meta_dat sample metadata as a data frame or tibble.
+#'   Must contain a `sample_ID` column.
+#'
+#' @return reneeDataSet object
+#' @export
+#'
+#' @examples
+#' sample_meta <- data.frame(
+#'   sample_id = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"),
+#'   condition = factor(
+#'     c("knockout", "knockout", "wildtype", "wildtype"),
+#'     levels = c("wildtype", "knockout")
+#'   )
+#' )
+#' reneeDataSetFromDataFrames(gene_counts, sample_meta)
+reneeDataSetFromDataFrames <- function(gene_counts_dat, sample_meta_dat) {
+  count_mat <- gene_counts_dat %>% counts_dat_to_matrix()
+  sample_meta_dat <- sample_meta_dat %>% meta_tbl_to_dat()
+
+  # sample IDs must be in the same order
+  if (!all(colnames(count_mat) == rownames(sample_meta_dat))) {
+    stop("Not all columns in the count matrix equal the rows in the sample metadata. Sample IDs must be in the same order.")
+  }
+
+  return(reneeDataSet(count_mat, sample_meta_dat))
+}
diff --git a/R/zzz.R b/R/zzz.R
new file mode 100644
index 0000000..3a6f2a2
--- /dev/null
+++ b/R/zzz.R
@@ -0,0 +1,9 @@
+# source: https://rconsortium.github.io/S7/articles/packages.html#method-registration
+.onLoad <- function(...) {
+  S7::methods_register()
+}
+
+# enable usage of <S7_object>@name in package code
+# source: https://rconsortium.github.io/S7/articles/packages.html#backward-compatibility
+#' @rawNamespace if (getRversion() < "4.3.0") importFrom("S7", "@")
+NULL
diff --git a/data-raw/gene_counts.R b/data-raw/gene_counts.R
index 6b68dc8..36d2942 100644
--- a/data-raw/gene_counts.R
+++ b/data-raw/gene_counts.R
@@ -1,3 +1,3 @@
 # WT_S1.RSEM.genes.results was generated from running RENEE v2.5.3 on the test dataset https://github.com/CCBR/RENEE/tree/e08f7db6c6e638cfd330caa182f64665d2ef37fa/.tests
-gene_counts <- readr::read_tsv("data-raw/RSEM.genes.expected_count.all_samples.txt")
+gene_counts <- readr::read_tsv(system.file("inst", "extdata", "RSEM.genes.expected_count.all_samples.txt", package = "reneeTools"))
 usethis::use_data(gene_counts, overwrite = TRUE)
diff --git a/data-raw/RSEM.genes.expected_count.all_samples.txt b/inst/extdata/RSEM.genes.expected_count.all_samples.txt
similarity index 100%
rename from data-raw/RSEM.genes.expected_count.all_samples.txt
rename to inst/extdata/RSEM.genes.expected_count.all_samples.txt
diff --git a/inst/extdata/sample_metadata.tsv b/inst/extdata/sample_metadata.tsv
new file mode 100644
index 0000000..48f3de4
--- /dev/null
+++ b/inst/extdata/sample_metadata.tsv
@@ -0,0 +1,5 @@
+sample_id	condition
+KO_S3	knockout
+KO_S4	knockout
+WT_S1	wildtype
+WT_S2	wildtype
diff --git a/man/counts_dat_to_matrix.Rd b/man/counts_dat_to_matrix.Rd
new file mode 100644
index 0000000..7f4917a
--- /dev/null
+++ b/man/counts_dat_to_matrix.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/counts.R
+\name{counts_dat_to_matrix}
+\alias{counts_dat_to_matrix}
+\title{Convert a data frame of gene counts to a matrix}
+\usage{
+counts_dat_to_matrix(counts_tbl)
+}
+\arguments{
+\item{counts_tbl}{expected gene counts from RSEM as a data frame or tibble.}
+}
+\value{
+matrix of gene counts with rows as gene IDs
+}
+\description{
+Convert a data frame of gene counts to a matrix
+}
+\examples{
+counts_dat_to_matrix(head(gene_counts))
+}
diff --git a/man/create_deseq_obj.Rd b/man/create_deseq_obj.Rd
deleted file mode 100644
index e0b3d83..0000000
--- a/man/create_deseq_obj.Rd
+++ /dev/null
@@ -1,30 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/deseq2.R
-\name{create_deseq_obj}
-\alias{create_deseq_obj}
-\title{Create DESeq2 object from gene counts and sample metadata}
-\usage{
-create_deseq_obj(counts_tbl, meta_dat, design)
-}
-\arguments{
-\item{counts_tbl}{expected gene counts from RSEM as a data frame or tibble.}
-
-\item{meta_dat}{sample metadata as a data frame with rownames as sample IDs.}
-
-\item{design}{model formula for experimental design. Columns must exist in \code{meta_dat}.}
-}
-\value{
-DESeqDataSet
-}
-\description{
-Create DESeq2 object from gene counts and sample metadata
-}
-\examples{
-sample_meta <- data.frame(
-  row.names = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"),
-  condition = factor(c("knockout", "knockout", "wildtype", "wildtype"),
-    levels = c("wildtype", "knockout")
-  )
-)
-dds <- create_deseq_obj(gene_counts, sample_meta, ~condition)
-}
diff --git a/man/meta_tbl_to_dat.Rd b/man/meta_tbl_to_dat.Rd
new file mode 100644
index 0000000..162cbd7
--- /dev/null
+++ b/man/meta_tbl_to_dat.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/metadata.R
+\name{meta_tbl_to_dat}
+\alias{meta_tbl_to_dat}
+\title{Convert sample metadata from a tibble to a dataframe with sample IDs as row names}
+\usage{
+meta_tbl_to_dat(meta_tbl)
+}
+\arguments{
+\item{meta_tbl}{tibble with \code{sample_id} column}
+}
+\value{
+dataframe where row names are the sample IDs
+}
+\description{
+Convert sample metadata from a tibble to a dataframe with sample IDs as row names
+}
+\examples{
+sample_meta_tbl <- readr::read_tsv(system.file("extdata",
+  "sample_metadata.tsv",
+  package = "reneeTools"
+))
+head(sample_meta_tbl)
+meta_tbl_to_dat(sample_meta_tbl)
+}
diff --git a/man/read_raw_counts.Rd b/man/read_raw_counts.Rd
deleted file mode 100644
index fb9fb09..0000000
--- a/man/read_raw_counts.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_raw_counts.R
-\name{read_raw_counts}
-\alias{read_raw_counts}
-\title{read_raw_counts}
-\usage{
-read_raw_counts(pathtofile, delimiter = "\\t")
-}
-\arguments{
-\item{pathtofile}{string absolute file path to raw counts matrix}
-
-\item{delimiter}{string default is tab}
-}
-\value{
-raw_counts_matrix
-}
-\description{
-read_raw_counts
-}
diff --git a/man/reneeDataSetFromDataFrames.Rd b/man/reneeDataSetFromDataFrames.Rd
new file mode 100644
index 0000000..f2f959d
--- /dev/null
+++ b/man/reneeDataSetFromDataFrames.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/renee-class.R
+\name{reneeDataSetFromDataFrames}
+\alias{reneeDataSetFromDataFrames}
+\title{Construct a reneeDataSet object from data frames}
+\usage{
+reneeDataSetFromDataFrames(gene_counts_dat, sample_meta_dat)
+}
+\arguments{
+\item{gene_counts_dat}{expected gene counts from RSEM as a data frame or tibble.
+Must contain a \code{gene_id} column and a column for each sample ID in the metadata.}
+
+\item{sample_meta_dat}{sample metadata as a data frame or tibble.
+Must contain a \code{sample_ID} column.}
+}
+\value{
+reneeDataSet object
+}
+\description{
+Construct a reneeDataSet object from data frames
+}
+\examples{
+sample_meta <- data.frame(
+  sample_id = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"),
+  condition = factor(
+    c("knockout", "knockout", "wildtype", "wildtype"),
+    levels = c("wildtype", "knockout")
+  )
+)
+reneeDataSetFromDataFrames(gene_counts, sample_meta)
+}
diff --git a/man/reneeDataSetFromFiles.Rd b/man/reneeDataSetFromFiles.Rd
new file mode 100644
index 0000000..5ecffe1
--- /dev/null
+++ b/man/reneeDataSetFromFiles.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/renee-class.R
+\name{reneeDataSetFromFiles}
+\alias{reneeDataSetFromFiles}
+\title{Construct a reneeDataSet object from tsv files.}
+\usage{
+reneeDataSetFromFiles(gene_counts_filepath, sample_meta_filepath)
+}
+\arguments{
+\item{gene_counts_filepath}{path to tsv file of expected gene counts from RSEM.}
+
+\item{sample_meta_filepath}{path to tsv file with sample IDs and metadata for differential analysis.}
+}
+\value{
+reneeDataSet object
+}
+\description{
+Construct a reneeDataSet object from tsv files.
+}
+\examples{
+reneeDataSetFromFiles(
+  system.file("extdata", "RSEM.genes.expected_count.all_samples.txt", package = "reneeTools"),
+  system.file("extdata", "sample_metadata.tsv", package = "reneeTools")
+)
+}
diff --git a/man/run_deseq2.Rd b/man/run_deseq2.Rd
new file mode 100644
index 0000000..8dd04b8
--- /dev/null
+++ b/man/run_deseq2.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/deseq2.R
+\name{run_deseq2}
+\alias{run_deseq2}
+\title{Run DESeq2 on a reneeDataSet}
+\usage{
+run_deseq2(renee_ds, design, ...)
+}
+\arguments{
+\item{renee_ds}{reneeDataSet object}
+
+\item{design}{model formula for experimental design. Columns must exist in \code{meta_dat}.}
+
+\item{...}{remaining variables are forwarded to \code{DESeq2::DESeq()}.}
+}
+\value{
+reneeDataSet object with DESeq2 slot filled
+}
+\description{
+Run DESeq2 on a reneeDataSet
+}
+\examples{
+rds <- reneeDataSetFromFiles(
+  system.file("extdata",
+    "RSEM.genes.expected_count.all_samples.txt",
+    package = "reneeTools"
+  ),
+  system.file("extdata", "sample_metadata.tsv",
+    package = "reneeTools"
+  )
+)
+run_deseq2(rds, ~condition)
+}
diff --git a/tests/testthat/test-deseq2.R b/tests/testthat/test-deseq2.R
index 321bb01..c62e2cb 100644
--- a/tests/testthat/test-deseq2.R
+++ b/tests/testthat/test-deseq2.R
@@ -1,26 +1,40 @@
 set.seed(20231228)
-test_that("create_deseq_obj works", {
-  sample_meta <-
-    data.frame(
-      row.names = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"),
-      condition = factor(
-        c("knockout", "knockout", "wildtype", "wildtype"),
-        levels = c("wildtype", "knockout")
-      )
+test_that("run_deseq2 works", {
+  renee_ds <- reneeDataSetFromFiles(
+    system.file(
+      "extdata",
+      "RSEM.genes.expected_count.all_samples.txt",
+      package = "reneeTools"
+    ),
+    system.file("extdata", "sample_metadata.tsv",
+      package = "reneeTools"
     )
-  dds <- create_deseq_obj(gene_counts, sample_meta, ~condition)
-
+  )
+  renee_ds@sample_meta <- renee_ds@sample_meta %>%
+    dplyr::mutate(condition = factor(condition,
+      levels = c("wildtype", "knockout")
+    ))
+  renee_ds <- run_deseq2(renee_ds, design = ~condition, fitType = "local")
+  dds <- renee_ds@analyses$deseq2_ds
   expect_equal(
     dds@colData %>% as.data.frame(),
     structure(
-      list(condition = structure(
-        c(2L, 2L, 1L, 1L),
-        levels = c(
-          "wildtype",
-          "knockout"
+      list(
+        condition = structure(
+          c(2L, 2L, 1L, 1L),
+          levels = c(
+            "wildtype",
+            "knockout"
+          ),
+          class = "factor"
         ),
-        class = "factor"
-      )),
+        sizeFactor = c(
+          0.759835685651593,
+          0.718608223926169,
+          1.24466595457696,
+          1.68179283050743
+        )
+      ),
       class = "data.frame",
       row.names = c(
         "KO_S3",
@@ -33,9 +47,31 @@ test_that("create_deseq_obj works", {
     structure(
       list(
         counts.KO_S3 = c(25L, 16L, 19L),
-        counts.KO_S4 = c(22L, 10L, 26L),
+        counts.KO_S4 = c(
+          22L,
+          10L, 26L
+        ),
         counts.WT_S1 = c(74L, 0L, 10L),
-        counts.WT_S2 = c(104L, 0L, 8L)
+        counts.WT_S2 = c(
+          104L,
+          0L, 8L
+        ),
+        mu.1 = c(24.1516682192168, 13.3092987017581, 23.1890203839711),
+        mu.2 = c(22.8412375617529, 12.5871575689046, 21.9308214491443),
+        mu.3 = c(75.6181929866826, 0.158242295472865, 7.74702804399805),
+        mu.4 = c(102.175314069834, 0.213817014139956, 10.4677854923446),
+        H.1 = c(0.511844332569779, 0.504138999697003, 0.50668916671393),
+        H.2 = c(0.48815561528062, 0.495860729372594, 0.493310737076545),
+        H.3 = c(0.454896663393873, 0.499997728127273, 0.447711231007698),
+        H.4 = c(0.545103297274594, 0.499997728127273, 0.552288438770429),
+        cooks.1 = c(
+          0.00787282712563543,
+          0.0262422886768066,
+          0.0478403297046226
+        ),
+        cooks.2 = c(0.00740399240405431, 0.025741204681852, 0.0464156166543046),
+        cooks.3 = c(0.00250160501520332, 0.127533456822227, 0.0779681548830785),
+        cooks.4 = c(0.00307311736197857, 0.161328557073165, 0.100411826759898)
       ),
       class = "data.frame",
       row.names = c(
diff --git a/tests/testthat/test-renee-class.R b/tests/testthat/test-renee-class.R
new file mode 100644
index 0000000..9193620
--- /dev/null
+++ b/tests/testthat/test-renee-class.R
@@ -0,0 +1,39 @@
+test_that("reneeDataSetFromFiles works", {
+  rds <- reneeDataSetFromFiles(
+    system.file("extdata", "RSEM.genes.expected_count.all_samples.txt", package = "reneeTools"),
+    system.file("extdata", "sample_metadata.tsv", package = "reneeTools")
+  )
+  expect_equal(
+    rds@counts %>% head(),
+    structure(c(
+      0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
+      0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L
+    ), dim = c(6L, 4L), dimnames = list(
+      c(
+        "ENSG00000121410.11", "ENSG00000268895.5", "ENSG00000148584.15",
+        "ENSG00000175899.14", "ENSG00000245105.3", "ENSG00000166535.20"
+      ), c("KO_S3", "KO_S4", "WT_S1", "WT_S2")
+    ))
+  )
+  expect_equal(
+    rds@sample_meta,
+    structure(list(condition = c(
+      "knockout", "knockout", "wildtype",
+      "wildtype"
+    )), row.names = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"), class = "data.frame")
+  )
+})
+
+test_that("reneeDataSetFromDataFrames detect problems", {
+  sample_meta <- data.frame(
+    sample_id = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"),
+    condition = factor(
+      c("knockout", "knockout", "wildtype", "wildtype"),
+      levels = c("wildtype", "knockout")
+    )
+  )
+  expect_error(
+    reneeDataSetFromDataFrames(gene_counts[, 1:4], sample_meta),
+    "Not all columns"
+  )
+})