1. singleCellTK
  2. man
  3. importCellRangerV2Sample.Rd
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Update dedup functionality for import data functions & update tutorial with VAM

Yichen Wang authored on 22/11/2021 17:57:17
Showing 1 changed files
man/importCellRangerV2Sample.Rd
History View file @ dfe50c33
... ... 
@@ -8,7 +8,8 @@ importCellRangerV2Sample(
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   dataDir = NULL,
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   sampleName = NULL,
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   class = c("Matrix", "matrix"),
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-  delayedArray = FALSE
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+  delayedArray = FALSE,
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+  rowNamesDedup = TRUE
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 )
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 }
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 \arguments{
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@@ -24,6 +25,9 @@ object. Can be one of "Matrix" (as returned by
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 \item{delayedArray}{Boolean. Whether to read the expression matrix as
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 \link{DelayedArray} object or not. Default \code{FALSE}.}
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+
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+\item{rowNamesDedup}{Boolean. Whether to deduplicate rownames. Default
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+\code{TRUE}.}
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 }
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 \value{
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 A \code{SingleCellExperiment} object containing the count
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Update importMitoGeneSet function. Change delayedArray=False for all import function. Minor fixs in QC HTML report

rz2333 authored on 30/12/2020 17:40:20
Showing 1 changed files
man/importCellRangerV2Sample.Rd
History View file @ 969718f9
... ... 
@@ -8,7 +8,7 @@ importCellRangerV2Sample(
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   dataDir = NULL,
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   sampleName = NULL,
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   class = c("Matrix", "matrix"),
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-  delayedArray = TRUE
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+  delayedArray = FALSE
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 )
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 }
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 \arguments{
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@@ -23,7 +23,7 @@ object. Can be one of "Matrix" (as returned by
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 \link[base]{matrix} function). Default "Matrix".}
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 \item{delayedArray}{Boolean. Whether to read the expression matrix as
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-\link{DelayedArray} object or not. Default \code{TRUE}.}
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+\link{DelayedArray} object or not. Default \code{FALSE}.}
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 }
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 \value{
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 A \code{SingleCellExperiment} object containing the count
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Edit links to documentation

unknown authored on 22/10/2020 03:39:09
Showing 1 changed files
man/importCellRangerV2Sample.Rd
History View file @ 6fe21ae1
... ... 
@@ -19,11 +19,11 @@ Default "sample".}
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 \item{class}{Character. The class of the expression matrix stored in the SCE
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 object. Can be one of "Matrix" (as returned by
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-\link[Matrix]{readMM} function), or "matrix" (as returned by
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+\link{readMM} function), or "matrix" (as returned by
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 \link[base]{matrix} function). Default "Matrix".}
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 \item{delayedArray}{Boolean. Whether to read the expression matrix as
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-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
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+\link{DelayedArray} object or not. Default \code{TRUE}.}
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 }
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 \value{
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 A \code{SingleCellExperiment} object containing the count
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Update importCellRangerV2 example data

rz2333 authored on 04/05/2020 15:28:25
Showing 1 changed files
man/importCellRangerV2Sample.Rd
History View file @ 73dfeffb
... ... 
@@ -36,7 +36,7 @@ Read the filtered barcodes, features, and matrices for all
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 }
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 \examples{
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 sce <- importCellRangerV2Sample(
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-    dataDir = system.file("extdata/pbmc_4k_v2_200x400/outs/",
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+    dataDir = system.file("extdata/pbmc_4k_v2_20x20/outs/",
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         "filtered_gene_bc_matrices/GRCh38", package = "singleCellTK"),
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-    sampleName = "pbmc400")
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+    sampleName = "pbmc4k_20")
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 }
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Merge conflict

rz2333 authored on 04/05/2020 02:25:09
Showing 1 changed files
man/importCellRangerV2Sample.Rd
History View file @ 4a58e6ab
... ... 
@@ -36,7 +36,7 @@ Read the filtered barcodes, features, and matrices for all
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 }
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 \examples{
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 sce <- importCellRangerV2Sample(
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-    dataDir = system.file("extdata/pbmc_4k_v2_200x800/pbmc_800/outs/",
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+    dataDir = system.file("extdata/pbmc_4k_v2_200x400/outs/",
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         "filtered_gene_bc_matrices/GRCh38", package = "singleCellTK"),
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-    sampleName = "pbmc800")
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+    sampleName = "pbmc400")
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 }
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Fix the bug in miscFunction (.convertToMatrix)

rz2333 authored on 23/04/2020 15:33:08
Showing 1 changed files
man/importCellRangerV2Sample.Rd
History View file @ 9f086cfb
... ... 
@@ -36,7 +36,7 @@ Read the filtered barcodes, features, and matrices for all
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 }
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 \examples{
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 sce <- importCellRangerV2Sample(
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-    dataDir = system.file("extdata/pbmc_4k_v2_200x800/outs/",
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+    dataDir = system.file("extdata/pbmc_4k_v2_200x800/pbmc_800/outs/",
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         "filtered_gene_bc_matrices/GRCh38", package = "singleCellTK"),
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     sampleName = "pbmc800")
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 }
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Fix exportSCEtoAnndata.R

rz2333 authored on 22/04/2020 17:34:30
Showing 1 changed files
man/importCellRangerV2Sample.Rd
History View file @ 7191c3e4
... ... 
@@ -36,7 +36,7 @@ Read the filtered barcodes, features, and matrices for all
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 }
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 \examples{
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 sce <- importCellRangerV2Sample(
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-    dataDir = system.file("extdata/pbmc_4k_v2_800/outs/",
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+    dataDir = system.file("extdata/pbmc_4k_v2_200x800/outs/",
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         "filtered_gene_bc_matrices/GRCh38", package = "singleCellTK"),
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     sampleName = "pbmc800")
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 }
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Fix importCellRangerV2, importCellRangerV2Sample, exportSCEtoTXT, SCTK_runQC.R and gmt files. Add pbmc800 dataset.

rz2333 authored on 31/03/2020 16:12:52
Showing 1 changed files
man/importCellRangerV2Sample.Rd
History View file @ 82a6da93
... ... 
@@ -5,14 +5,14 @@
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 \title{Construct SCE object from Cell Ranger V2 output for a single sample}
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 \usage{
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 importCellRangerV2Sample(
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-  sampleDir = NULL,
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+  dataDir = NULL,
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   sampleName = NULL,
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   class = c("Matrix", "matrix"),
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   delayedArray = TRUE
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 )
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 }
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 \arguments{
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-\item{sampleDir}{A path to the directory containing the data files. Default "./".}
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+\item{dataDir}{A path to the directory containing the data files. Default "./".}
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 \item{sampleName}{A User-defined sample name. This will be prepended to all cell barcode IDs.
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 Default "sample".}
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@@ -31,6 +31,12 @@ A \code{SingleCellExperiment} object containing the count
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 }
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 \description{
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 Read the filtered barcodes, features, and matrices for all
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- samples from Cell Ranger V3 output. Files are assumed to be named
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+ samples from Cell Ranger V2 output. Files are assumed to be named
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  "matrix.mtx", "genes.tsv", and "barcodes.tsv".
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 }
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+\examples{
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+sce <- importCellRangerV2Sample(
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+    dataDir = system.file("extdata/pbmc_4k_v2_800/outs/",
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+        "filtered_gene_bc_matrices/GRCh38", package = "singleCellTK"),
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+    sampleName = "pbmc800")
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+}
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Updated LIGER function and put correct dependencies in DESCRIPTION. Updated docs

Joshua D. Campbell authored on 06/03/2020 05:15:13
Showing 1 changed files
man/importCellRangerV2Sample.Rd
History View file @ 64d3a71f
... ... 
@@ -4,8 +4,12 @@
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 \alias{importCellRangerV2Sample}
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 \title{Construct SCE object from Cell Ranger V2 output for a single sample}
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 \usage{
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-importCellRangerV2Sample(sampleDir = NULL, sampleName = NULL,
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-  class = c("Matrix", "matrix"), delayedArray = TRUE)
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+importCellRangerV2Sample(
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+  sampleDir = NULL,
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+  sampleName = NULL,
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+  class = c("Matrix", "matrix"),
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+  delayedArray = TRUE
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+)
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 }
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 \arguments{
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 \item{sampleDir}{A path to the directory containing the data files. Default "./".}
Browse code

move to branch

Yichen Wang authored on 04/03/2020 20:32:17
Showing 1 changed files
man/importCellRangerV2Sample.Rd
History View file @ e624033d
... ... 
@@ -4,12 +4,8 @@
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 \alias{importCellRangerV2Sample}
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 \title{Construct SCE object from Cell Ranger V2 output for a single sample}
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 \usage{
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-importCellRangerV2Sample(
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-  sampleDir = NULL,
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-  sampleName = NULL,
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-  class = c("Matrix", "matrix"),
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-  delayedArray = TRUE
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-)
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+importCellRangerV2Sample(sampleDir = NULL, sampleName = NULL,
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+  class = c("Matrix", "matrix"), delayedArray = TRUE)
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 }
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 \arguments{
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 \item{sampleDir}{A path to the directory containing the data files. Default "./".}
Browse code

Fixed errors/warnings in DoubletFinder code. Updated docs. Added documentation for importCellRangerV2/V3Sample functions. Added install of DoubletFinder from github in DESCRIPTION and in .travis.yml

Joshua D. Campbell authored on 15/02/2020 00:05:10
Showing 1 changed files
man/importCellRangerV2Sample.Rd
History View file @ 8a33a64b
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new file mode 100644
... ... 
@@ -0,0 +1,36 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/importCellRanger.R
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+\name{importCellRangerV2Sample}
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+\alias{importCellRangerV2Sample}
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+\title{Construct SCE object from Cell Ranger V2 output for a single sample}
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+\usage{
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+importCellRangerV2Sample(
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+  sampleDir = NULL,
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+  sampleName = NULL,
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+  class = c("Matrix", "matrix"),
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+  delayedArray = TRUE
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+)
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+}
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+\arguments{
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+\item{sampleDir}{A path to the directory containing the data files. Default "./".}
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+
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+\item{sampleName}{A User-defined sample name. This will be prepended to all cell barcode IDs.
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+Default "sample".}
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+
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+\item{class}{Character. The class of the expression matrix stored in the SCE
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+object. Can be one of "Matrix" (as returned by
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+\link[Matrix]{readMM} function), or "matrix" (as returned by
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+\link[base]{matrix} function). Default "Matrix".}
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+
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+\item{delayedArray}{Boolean. Whether to read the expression matrix as
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+\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
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+}
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+\value{
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+A \code{SingleCellExperiment} object containing the count
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+ matrix, the feature annotations, and the cell annotation for the sample.
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+}
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+\description{
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+Read the filtered barcodes, features, and matrices for all
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+ samples from Cell Ranger V3 output. Files are assumed to be named
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+ "matrix.mtx", "genes.tsv", and "barcodes.tsv".
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+}