feat: add bambu.singlecell and bambu.spatial wrapper functions

Author: ch99l

NAMESPACE

@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 export(bambu)
+export(bambu.singlecell)
+export(bambu.spatial)
 export(plotBambu)
 export(prepareAnnotations)
 export(readFromGTF)

R/bambu.R

@@ -317,4 +317,78 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
         }
         return(countsSe)
     }
-  }
+  }
+
+#' Single-cell wrapper for bambu
+#' @title Single-cell isoform reconstruction and quantification
+#' @description Wrapper around \code{\link{bambu}} for single-cell data.
+#' Accepts an \code{opt.singlecell} list for single-cell specific parameters
+#' and passes all other arguments directly to \code{\link{bambu}}.
+#' @param opt.singlecell A list of single-cell specific parameters:
+#' \describe{
+#'     \item{extractBarcodeUMI}{Logical, whether to extract cell barcodes and
+#'     UMIs from BAM tags or read names. Defaults to FALSE}
+#'     \item{dedupUMI}{Logical, whether to perform UMI-based deduplication per
+#'     barcode. Defaults to FALSE}
+#'     \item{clusters}{A named list mapping cluster names to barcode vectors,
+#'     used for cluster-level transcript discovery. Defaults to NULL}
+#' }
+#' @inheritParams bambu
+#' @export
+bambu.singlecell <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
+    mode = NULL, opt.discovery = NULL, opt.em = NULL, opt.singlecell = NULL,
+    rcOutDir = NULL, discovery = TRUE, assignDist = TRUE, quant = TRUE,
+    stranded = FALSE, ncore = 1, yieldSize = NULL, trackReads = FALSE,
+    returnDistTable = FALSE, lowMemory = FALSE, sampleData = NULL,
+    fusionMode = FALSE, verbose = FALSE, quantData = NULL,
+    processByChromosome = FALSE, processByBam = TRUE) {
+    extractBarcodeUMI <- isTRUE(opt.singlecell$extractBarcodeUMI)
+    dedupUMI <- isTRUE(opt.singlecell$dedupUMI)
+    clusters <- opt.singlecell$clusters
+    bambu(reads = reads, annotations = annotations, genome = genome, NDR = NDR,
+        mode = mode, opt.discovery = opt.discovery, opt.em = opt.em,
+        rcOutDir = rcOutDir, discovery = discovery, assignDist = assignDist,
+        quant = quant, stranded = stranded, ncore = ncore, yieldSize = yieldSize,
+        trackReads = trackReads, returnDistTable = returnDistTable,
+        lowMemory = lowMemory, sampleData = sampleData, fusionMode = fusionMode,
+        verbose = verbose, extractBarcodeUMI = extractBarcodeUMI,
+        quantData = quantData, dedupUMI = dedupUMI, clusters = clusters,
+        processByChromosome = processByChromosome, processByBam = processByBam)
+}
+
+#' Spatial wrapper for bambu
+#' @title Spatial isoform reconstruction and quantification
+#' @description Wrapper around \code{\link{bambu}} for spatial transcriptomics
+#' data. Accepts an \code{opt.spatial} list for spatial specific parameters
+#' and passes all other arguments directly to \code{\link{bambu}}.
+#' @param opt.spatial A list of spatial specific parameters:
+#' \describe{
+#'     \item{extractBarcodeUMI}{Logical, whether to extract spot barcodes and
+#'     UMIs from BAM tags or read names. Defaults to FALSE}
+#'     \item{dedupUMI}{Logical, whether to perform UMI-based deduplication per
+#'     barcode. Defaults to FALSE}
+#'     \item{clusters}{A named list mapping cluster names to barcode vectors,
+#'     used for cluster-level transcript discovery. Defaults to NULL}
+#' }
+#' @inheritParams bambu
+#' @export
+bambu.spatial <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
+    mode = NULL, opt.discovery = NULL, opt.em = NULL, opt.spatial = NULL,
+    rcOutDir = NULL, discovery = TRUE, assignDist = TRUE, quant = TRUE,
+    stranded = FALSE, ncore = 1, yieldSize = NULL, trackReads = FALSE,
+    returnDistTable = FALSE, lowMemory = FALSE, sampleData = NULL,
+    fusionMode = FALSE, verbose = FALSE, quantData = NULL,
+    processByChromosome = FALSE, processByBam = TRUE) {
+    extractBarcodeUMI <- isTRUE(opt.spatial$extractBarcodeUMI)
+    dedupUMI <- isTRUE(opt.spatial$dedupUMI)
+    clusters <- opt.spatial$clusters
+    bambu(reads = reads, annotations = annotations, genome = genome, NDR = NDR,
+        mode = mode, opt.discovery = opt.discovery, opt.em = opt.em,
+        rcOutDir = rcOutDir, discovery = discovery, assignDist = assignDist,
+        quant = quant, stranded = stranded, ncore = ncore, yieldSize = yieldSize,
+        trackReads = trackReads, returnDistTable = returnDistTable,
+        lowMemory = lowMemory, sampleData = sampleData, fusionMode = fusionMode,
+        verbose = verbose, extractBarcodeUMI = extractBarcodeUMI,
+        quantData = quantData, dedupUMI = dedupUMI, clusters = clusters,
+        processByChromosome = processByChromosome, processByBam = processByBam)
+}