feat: create reneeDataSet class

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ exclude: |
   (?x)(
       ^assets/|
       ^docs/.*.html|
-      ^data-raw/*.txt|
+      ^inst/extdata|
       ^man/
    )
 repos:

DESCRIPTION

@@ -19,6 +19,7 @@ Imports:
     assertthat,
     DESeq2,
     dplyr,
+    S7,
     tidyr
 Suggests:
     readr,

NAMESPACE

@@ -1,7 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
+export(counts_dat_to_matrix)
 export(create_deseq_obj)
 export(filter_low_counts)
-export(read_raw_counts)
+export(meta_tbl_to_dat)
+export(reneeDataSetFromFiles)
+export(run_deseq2)
+if (getRversion() < "4.3.0") importFrom("S7", "@")
 importFrom(dplyr,"%>%")

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)
+}

R/deseq2.R

@@ -16,22 +16,40 @@
 #' )
 #' 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()
+  counts_mat <- counts_dat_to_matrix(counts_tbl)
 
   # 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 on a reneeDataSet
+#'
+#' @param renee_ds reneeDataSet object
+#' @param design   model formula for experimental design. Columns must exist in `meta_dat`.
+#'
+#' @return reneeDataSet object with DESeq2 slot filled
+#' @export
+#'
+#' @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)
+run_deseq2 <- function(renee_ds, design) {
+  dds <- DESeq2::DESeqDataSetFromMatrix(
+    renee_ds$counts,
+    renee_ds$sample_meta,
+    design
+  )
+  renee_ds$deseq2 <- DESeq2::DESeq(dds)
+  return(renee_ds)
+}

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)
+}

R/renee-class.R

@@ -0,0 +1,34 @@
+reneeDataSet <- S7::new_class("renee",
+  parent = S7::class_list,
+  constructor = function(count_matrix, sample_meta_dat) {
+    S7::new_object(list(
+      counts = count_matrix,
+      sample_meta = sample_meta_dat
+    ))
+  }
+)
+
+#' Create 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_mat <- readr::read_tsv(gene_counts_filepath) %>%
+    counts_dat_to_matrix()
+  sample_meta_dat <- readr::read_tsv(sample_meta_filepath) %>%
+    meta_tbl_to_dat()
+
+  # sample IDs must be in the same order
+  assertthat::are_equal(colnames(count_mat), rownames(sample_meta_dat))
+
+  return(reneeDataSet(count_mat, sample_meta_dat))
+}

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

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)

inst/extdata/sample_metadata.tsv

@@ -0,0 +1,5 @@
+sample_id	condition
+KO_S3	knockout
+KO_S4	knockout
+WT_S1	wildtype
+WT_S2	wildtype