1. singleCellTK
  2. man
  3. getSampleSummaryStatsTable.Rd
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Fix R CMD CHECK warning

Yichen Wang authored on 29/09/2022 08:58:00
Showing 1 changed files
man/getSampleSummaryStatsTable.Rd
History View file @ ae4bffec
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@@ -24,6 +24,9 @@ that stores the stats table within the metadata of the
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 SingleCellExperiment object. Required.}
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 \item{...}{Other arguments passed to the function.}
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+
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+\item{value}{The summary table for QC statistics generated from SingleCellTK
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+to be added to the SCE object.}
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 }
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 \value{
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 For \code{getSampleSummaryStatsTable}, A matrix/array object.
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Fix Rd man warnings

Yichen Wang authored on 29/09/2022 03:01:51
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man/getSampleSummaryStatsTable.Rd
History View file @ 8b21d375
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@@ -2,12 +2,18 @@
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 % Please edit documentation in R/allGenerics.R, R/sampleSummaryStats.R
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 \name{getSampleSummaryStatsTable}
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 \alias{getSampleSummaryStatsTable}
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+\alias{setSampleSummaryStatsTable<-}
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 \alias{getSampleSummaryStatsTable,SingleCellExperiment-method}
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+\alias{setSampleSummaryStatsTable<-,SingleCellExperiment-method}
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 \title{Stores and returns table of SCTK QC outputs to metadata.}
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 \usage{
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 getSampleSummaryStatsTable(inSCE, statsName, ...)
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+setSampleSummaryStatsTable(inSCE, statsName, ...) <- value
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+
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 \S4method{getSampleSummaryStatsTable}{SingleCellExperiment}(inSCE, statsName, ...)
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+
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+\S4method{setSampleSummaryStatsTable}{SingleCellExperiment}(inSCE, statsName, ...) <- value
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 }
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 \arguments{
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 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved
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@@ -20,8 +26,10 @@ SingleCellExperiment object. Required.}
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 \item{...}{Other arguments passed to the function.}
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 }
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 \value{
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-A matrix/array object. Contains a summary table for QC statistics
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-generated from SingleCellTK.
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+For \code{getSampleSummaryStatsTable}, A matrix/array object.
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+Contains a summary table for QC statistics generated from SingleCellTK. For
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+\code{setSampleSummaryStatsTable<-}, A SingleCellExperiment object where the
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+summary table is updated in the \code{metadata} slot.
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 }
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 \description{
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 Stores and returns table of QC metrics generated from
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Document ... argument in get/list/setSampleSummaryStatsTable. Add rstantools in DESCRIPTION to avoid dependencies in github workflow check

rz2333 authored on 21/02/2022 22:26:18
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man/getSampleSummaryStatsTable.Rd
History View file @ 760fa304
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@@ -16,6 +16,8 @@ getSampleSummaryStatsTable(inSCE, statsName, ...)
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 \item{statsName}{A \code{character} value indicating the slot
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 that stores the stats table within the metadata of the
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 SingleCellExperiment object. Required.}
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+
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+\item{...}{Other arguments passed to the function.}
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 }
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 \value{
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 A matrix/array object. Contains a summary table for QC statistics
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Edits to sampleSummaryStatsTable; setter/getter functions now have set/get prefixes

Yusuke Koga authored on 09/02/2022 13:50:44
Showing 1 changed files
man/getSampleSummaryStatsTable.Rd
History View file @ 5551acab
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new file mode 100644
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@@ -0,0 +1,33 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/allGenerics.R, R/sampleSummaryStats.R
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+\name{getSampleSummaryStatsTable}
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+\alias{getSampleSummaryStatsTable}
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+\alias{getSampleSummaryStatsTable,SingleCellExperiment-method}
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+\title{Stores and returns table of SCTK QC outputs to metadata.}
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+\usage{
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+getSampleSummaryStatsTable(inSCE, statsName, ...)
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+
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+\S4method{getSampleSummaryStatsTable}{SingleCellExperiment}(inSCE, statsName, ...)
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+}
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+\arguments{
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+\item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved
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+\link{assay} data and/or \link{colData} data. Required.}
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+
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+\item{statsName}{A \code{character} value indicating the slot
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+that stores the stats table within the metadata of the
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+SingleCellExperiment object. Required.}
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+}
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+\value{
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+A matrix/array object. Contains a summary table for QC statistics
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+generated from SingleCellTK.
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+}
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+\description{
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+Stores and returns table of QC metrics generated from
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+ QC algorithms within the metadata slot of the SingleCellExperiment object.
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+}
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+\examples{
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+data(scExample, package = "singleCellTK")
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+sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
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+sce <- sampleSummaryStats(sce, simple = TRUE, statsName = "qc_table")
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+getSampleSummaryStatsTable(sce, statsName = "qc_table")
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+}