add ReadParseBio

NAMESPACE

@@ -264,6 +264,7 @@ export(Read10X)
 export(Read10X_Image)
 export(Read10X_h5)
 export(ReadMtx)
+export(ReadParseBio)
 export(ReadSTARsolo)
 export(ReadSlideSeq)
 export(Reductions)

R/convenience.R

@@ -172,16 +172,41 @@ SpecificDimPlot <- function(object, ...) {
   )
 }
 
+#' Read output from Parse Biosciences
+#'
+#' @param data.dir Directory containing the data files
+#' @param ... Extra parameters passed to \code{\link{ReadMtx}}
+#' @concept convenience
+#' @export
+#'
+ReadParseBio <- function(data.dir, ...) {
+  mtx <- file.path(data.dir, "DGE.mtx")
+  cells <- file.path(data.dir, "cell_metadata.csv")
+  features <- file.path(data.dir, "genes.csv")
+  return(ReadMtx(
+    mtx = mtx,
+    cells = cells,
+    features = features,
+    cell.column = 1,
+    feature.column = 2,
+    cell.sep = ",",
+    feature.sep = ",",
+    skip.cell = 1,
+    skip.feature = 1,
+    mtx.transpose = TRUE
+  ))
+}
+
 #' Read output from STARsolo
 #'
 #' @param data.dir Directory containing the data files
-#' @param ... Extra parameters passed to \code{ReadMtx}
+#' @param ... Extra parameters passed to \code{\link{ReadMtx}}
 #'
 #' @rdname ReadSTARsolo
 #' @concept convenience
 #' @export
 #'
-ReadSTARsolo <- function(data.dir, ... ){
+ReadSTARsolo <- function(data.dir, ... ) {
   mtx <- file.path(data.dir, "matrix.mtx")
   cells <- file.path(data.dir, "barcodes.tsv")
   features <- file.path(data.dir, "features.tsv")

R/preprocessing.R

@@ -1045,8 +1045,11 @@ Read10X_Image <- function(image.dir, image.name = "tissue_lowres_image.png", fil
 #' @param features Name or remote URL of the features/genes file
 #' @param cell.column Specify which column of cells file to use for cell names; default is 1
 #' @param feature.column Specify which column of features files to use for feature/gene names; default is 2
+#' @param cell.sep Specify the delimiter in the cell name file
+#' @param feature.sep Specify the delimiter in the feature name file
 #' @param skip.cell Number of lines to skip in the cells file before beginning to read cell names
 #' @param skip.feature Number of lines to skip in the features file before beginning to gene names
+#' @param mtx.transpose Transpose the matrix after reading in
 #' @param unique.features Make feature names unique (default TRUE)
 #' @param strip.suffix Remove trailing "-1" if present in all cell barcodes.
 #'
@@ -1085,8 +1088,11 @@ ReadMtx <- function(
   features,
   cell.column = 1,
   feature.column = 2,
+  cell.sep = "\t",
+  feature.sep = "\t",
   skip.cell = 0,
   skip.feature = 0,
+  mtx.transpose = FALSE,
   unique.features = TRUE,
   strip.suffix = FALSE
 ) {
@@ -1118,14 +1124,14 @@ ReadMtx <- function(
   cell.barcodes <- read.table(
     file = all.files[['barcode list']],
     header = FALSE,
-    sep = '\t',
+    sep = cell.sep,
     row.names = NULL,
     skip = skip.cell
   )
   feature.names <- read.table(
     file = all.files[['feature list']],
     header = FALSE,
-    sep = '\t',
+    sep = feature.sep,
     row.names = NULL,
     skip = skip.feature
   )
@@ -1196,6 +1202,9 @@ ReadMtx <- function(
     feature.names <- make.unique(names = feature.names)
   }
   data <- readMM(file = all.files[['expression matrix']])
+  if (mtx.transpose) {
+    data <- t(x = data)
+  }
   if (length(x = cell.names) != ncol(x = data)) {
     stop(
       "Matrix has ",