1. singleCellTK
  2. man
  3. combineSCE.Rd
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Fixed R CMD check issues

Irzam Sarfraz authored on 20/12/2021 22:24:01
Showing 1 changed files
man/combineSCE.Rd
History View file @ c36924bf
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@@ -30,5 +30,6 @@ objects in sceList. The colData is merged.
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 Combine a list of SingleCellExperiment objects as one SingleCellExperiment object
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 }
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 \examples{
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+data(scExample, package = "singleCellTK")
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 combinedsce <- combineSCE(list(sce,sce), by.r = NULL, by.c = NULL, combined = TRUE)
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 }
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Fix bugs in combineSCE. Update SCTK_runQC.R to include an col in colData indicate whether a barcode is a true cell in the cellSCE object. Update QC documentation

rz2333 authored on 22/09/2021 20:21:28
Showing 1 changed files
man/combineSCE.Rd
History View file @ 431c970b
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@@ -4,18 +4,23 @@
4 4 
 \alias{combineSCE}
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 \title{Combine a list of SingleCellExperiment objects as one SingleCellExperiment object}
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 \usage{
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-combineSCE(sceList, by.r, by.c, combined)
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+combineSCE(sceList, by.r = NULL, by.c = NULL, combined = TRUE)
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 }
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 \arguments{
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 \item{sceList}{A list contains \link[SingleCellExperiment]{SingleCellExperiment} objects.
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 Currently, combineSCE function only support combining SCE objects with assay in dgCMatrix format.
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 It does not support combining SCE with assay in delayedArray format.}
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-\item{by.r}{Specifications of the columns used for merging rowData. See 'Details'.}
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+\item{by.r}{Specifications of the columns used for merging rowData. If set as NULL,
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+the rownames of rowData tables will be used to merging rowData. Default is NULL.}
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-\item{by.c}{Specifications of the columns used for merging colData. See 'Details'.}
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+\item{by.c}{Specifications of the columns used for merging colData. If set as NULL,
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+the rownames of colData tables will be used to merging colData. Default is NULL.}
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-\item{combined}{logical; if TRUE, it will combine the list of SingleCellExperiment objects. See 'Details'.}
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+\item{combined}{logical; if TRUE, it will combine the list of SingleCellExperiment objects
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+and return a SingleCellExperiment. If FALSE, it will return a list of SingleCellExperiment whose
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+rowData, colData, assay and reducedDim data slot are compatible within SCE objects in the list.
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+Default is TRUE.}
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 }
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 \value{
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 A \link[SingleCellExperiment]{SingleCellExperiment} object which combines all
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UI update for previous related DE function update; plus many minor bug fixes

Yichen Wang authored on 17/03/2021 16:51:52
Showing 1 changed files
man/combineSCE.Rd
History View file @ ea2808fc
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@@ -7,8 +7,8 @@
7 7 
 combineSCE(sceList, by.r, by.c, combined)
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 }
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 \arguments{
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-\item{sceList}{A list contains \link[SingleCellExperiment]{SingleCellExperiment} objects.
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-Currently, combineSCE function only support combining SCE objects with assay in dgCMatrix format.
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+\item{sceList}{A list contains \link[SingleCellExperiment]{SingleCellExperiment} objects.
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+Currently, combineSCE function only support combining SCE objects with assay in dgCMatrix format.
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 It does not support combining SCE with assay in delayedArray format.}
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 \item{by.r}{Specifications of the columns used for merging rowData. See 'Details'.}
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Update documentation for combineSCE.R

rz2333 authored on 21/10/2020 19:50:42
Showing 1 changed files
man/combineSCE.Rd
History View file @ 5daf7de2
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@@ -7,7 +7,9 @@
7 7 
 combineSCE(sceList, by.r, by.c, combined)
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 }
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 \arguments{
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-\item{sceList}{A list contains \link[SingleCellExperiment]{SingleCellExperiment} objects}
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+\item{sceList}{A list contains \link[SingleCellExperiment]{SingleCellExperiment} objects.
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+Currently, combineSCE function only support combining SCE objects with assay in dgCMatrix format.
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+It does not support combining SCE with assay in delayedArray format.}
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 \item{by.r}{Specifications of the columns used for merging rowData. See 'Details'.}
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Add Runnable functions

Yusuke Koga authored on 15/10/2020 16:44:51
Showing 1 changed files
man/combineSCE.Rd
History View file @ 0ccddee1
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@@ -16,9 +16,12 @@ combineSCE(sceList, by.r, by.c, combined)
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 \item{combined}{logical; if TRUE, it will combine the list of SingleCellExperiment objects. See 'Details'.}
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 }
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 \value{
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-A \link[SingleCellExperiment]{SingleCellExperiment} object which combines all
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+A \link[SingleCellExperiment]{SingleCellExperiment} object which combines all
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 objects in sceList. The colData is merged.
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 }
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 \description{
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 Combine a list of SingleCellExperiment objects as one SingleCellExperiment object
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 }
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+\examples{
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+combinedsce <- combineSCE(list(sce,sce), by.r = NULL, by.c = NULL, combined = TRUE)
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+}
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Update combineSCE function to merge metadata slot. Update runBarcodeRank and its plotting function

rz2333 authored on 29/09/2020 03:48:43
Showing 1 changed files
man/combineSCE.Rd
History View file @ feff3b1d
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@@ -1,13 +1,19 @@
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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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+% Please edit documentation in R/combineSCE.R
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 \name{combineSCE}
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 \alias{combineSCE}
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 \title{Combine a list of SingleCellExperiment objects as one SingleCellExperiment object}
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 \usage{
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-combineSCE(sceList)
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+combineSCE(sceList, by.r, by.c, combined)
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 }
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 \arguments{
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 \item{sceList}{A list contains \link[SingleCellExperiment]{SingleCellExperiment} objects}
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+
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+\item{by.r}{Specifications of the columns used for merging rowData. See 'Details'.}
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+
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+\item{by.c}{Specifications of the columns used for merging colData. See 'Details'.}
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+
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+\item{combined}{logical; if TRUE, it will combine the list of SingleCellExperiment objects. See 'Details'.}
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 }
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 \value{
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 A \link[SingleCellExperiment]{SingleCellExperiment} object which combines all
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Organize SCTK_runQC.R and move utility functions into R/sctkQCUtils.R

rz2333 authored on 25/05/2020 17:23:03
Showing 1 changed files
man/combineSCE.Rd
History View file @ ece1f3d8
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new file mode 100644
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@@ -0,0 +1,18 @@
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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{combineSCE}
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+\alias{combineSCE}
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+\title{Combine a list of SingleCellExperiment objects as one SingleCellExperiment object}
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+\usage{
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+combineSCE(sceList)
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+}
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+\arguments{
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+\item{sceList}{A list contains \link[SingleCellExperiment]{SingleCellExperiment} objects}
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+}
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+\value{
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+A \link[SingleCellExperiment]{SingleCellExperiment} object which combines all
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+objects in sceList. The colData is merged.
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+}
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+\description{
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+Combine a list of SingleCellExperiment objects as one SingleCellExperiment object
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+}