Ming Liu authored on 05/01/2024 20:34:37
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@@ -13,6 +13,7 @@ qcInputProcess( |
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ref, |
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rawFile, |
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filFile, |
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+ flatFiles, |
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dataType |
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) |
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} |
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@@ -33,6 +34,8 @@ qcInputProcess( |
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\item{filFile}{The full path of the RDS file or Matrix file of the cell count matrix. It's one of the path provided in --cell_data argument.}
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+\item{flatFiles}{The full paths of the matrix, barcode, and features (in that order) files used to construct an SCE object.}
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+ |
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\item{dataType}{Type of the input. It can be "Both", "Droplet" or "Cell". It's one of the path provided in --genome argument.}
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} |
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\value{
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rz2333 authored on 23/06/2020 23:27:49
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@@ -17,6 +17,8 @@ qcInputProcess( |
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) |
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} |
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\arguments{
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+\item{preproc}{Method used to preprocess the data. It's one of the path provided in --preproc argument.}
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+ |
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\item{samplename}{The sample name of the data. It's one of the path provided in --sample argument.}
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\item{path}{Base path of the dataset. It's one of the path provided in --bash_path argument.}
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rz2333 authored on 22/06/2020 17:48:28
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new file mode 100644 |
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@@ -0,0 +1,42 @@ |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/sctkQCUtils.R |
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+\name{qcInputProcess}
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+\alias{qcInputProcess}
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+\title{Create SingleCellExperiment object from command line input arguments}
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+\usage{
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+qcInputProcess( |
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+ preproc, |
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+ samplename, |
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+ path, |
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+ raw, |
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+ fil, |
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+ ref, |
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+ rawFile, |
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+ filFile, |
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+ dataType |
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+) |
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+} |
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+\arguments{
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+\item{samplename}{The sample name of the data. It's one of the path provided in --sample argument.}
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+ |
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+\item{path}{Base path of the dataset. It's one of the path provided in --bash_path argument.}
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+ |
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+\item{raw}{The directory contains droplet matrix, gene and cell barcodes information. It's one of the path provided in --raw_data_path argument.}
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+ |
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+\item{fil}{The directory contains cell matrix, gene and cell barcodes information. It's one of the path provided in --cell_data_path argument.}
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+ |
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+\item{ref}{The name of reference used by cellranger. Only need for CellrangerV2 data.}
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+ |
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+\item{rawFile}{The full path of the RDS file or Matrix file of the raw gene count matrix. It's one of the path provided in --raw_data argument.}
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+ |
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+\item{filFile}{The full path of the RDS file or Matrix file of the cell count matrix. It's one of the path provided in --cell_data argument.}
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+ |
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+\item{dataType}{Type of the input. It can be "Both", "Droplet" or "Cell". It's one of the path provided in --genome argument.}
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+} |
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+\value{
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+A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing
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+the droplet or cell data or both,depending on the dataType that users provided. |
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+} |
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+\description{
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+Create SingleCellExperiment object from command line input arguments |
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+} |