1. singleCellTK
  2. man
  3. calcEffectSizes.Rd
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local BiocCheck error fix

Yichen Wang authored on 10/05/2021 22:58:10
Showing 1 changed files
man/calcEffectSizes.Rd
History View file @ 930ec858
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@@ -24,6 +24,6 @@ significance.
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 \examples{
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 data("mouseBrainSubsetSCE")
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 res <- calcEffectSizes(assay(mouseBrainSubsetSCE, "counts"),
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-                       condition = colData(mouseBrainSubsetSCE)[, "level1class"])
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+                       condition = colData(mouseBrainSubsetSCE)$level1class)
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 }
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Consistent use of camel case throughout the app

David Jenkins authored on 06/04/2018 20:11:01
Showing 1 changed files
man/calcEffectSizes.Rd
History View file @ c32ed94f
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@@ -1,5 +1,5 @@
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 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/Downsample.Matrix.R
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+% Please edit documentation in R/DownsampleMatrix.R
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 \name{calcEffectSizes}
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 \alias{calcEffectSizes}
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 \title{Finds the effect sizes for all genes in the original dataset, regardless of
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@@ -22,8 +22,8 @@ Finds the effect sizes for all genes in the original dataset, regardless of
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 significance.
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 }
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 \examples{
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-data("mouse_brain_subset_sce")
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-res <- calcEffectSizes(assay(mouse_brain_subset_sce, "counts"),
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-                       condition = colData(mouse_brain_subset_sce)[, "level1class"])
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+data("mouseBrainSubsetSCE")
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+res <- calcEffectSizes(assay(mouseBrainSubsetSCE, "counts"),
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+                       condition = colData(mouseBrainSubsetSCE)[, "level1class"])
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 }
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Removed examples that weren't being used. Updated requirement to 3.5 for bioconductor release, changednged the name of the GSE60361 dataset to be more descriptive. Added a link to the data source. Fixed DESeq2 bug. Version bump

David Jenkins authored on 20/03/2018 23:51:57
Showing 1 changed files
man/calcEffectSizes.Rd
History View file @ 50eb6908
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@@ -22,8 +22,8 @@ Finds the effect sizes for all genes in the original dataset, regardless of
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 significance.
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 }
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 \examples{
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-data("GSE60361_subset_sce")
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-res <- calcEffectSizes(assay(GSE60361_subset_sce, "counts"),
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-                       condition = colData(GSE60361_subset_sce)[, "level1class"])
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+data("mouse_brain_subset_sce")
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+res <- calcEffectSizes(assay(mouse_brain_subset_sce, "counts"),
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+                       condition = colData(mouse_brain_subset_sce)[, "level1class"])
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 }
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Updates to pass BiocCheck

David Jenkins authored on 22/02/2018 23:37:15
Showing 1 changed files
man/calcEffectSizes.Rd
History View file @ 1db9e48a
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@@ -21,3 +21,9 @@ A vector of cohen's d effect sizes for each gene.
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 Finds the effect sizes for all genes in the original dataset, regardless of
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 significance.
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 }
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+\examples{
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+data("GSE60361_subset_sce")
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+res <- calcEffectSizes(assay(GSE60361_subset_sce, "counts"),
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+                       condition = colData(GSE60361_subset_sce)[, "level1class"])
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+
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+}
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Documentation updates to add examples and fix indentation

David Jenkins authored on 16/02/2018 22:45:56
Showing 1 changed files
man/calcEffectSizes.Rd
History View file @ 40c2c313
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@@ -2,18 +2,22 @@
2 2 
 % Please edit documentation in R/Downsample.Matrix.R
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 \name{calcEffectSizes}
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 \alias{calcEffectSizes}
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-\title{Finds the effect sizes for all genes in the original dataset, regardless of significance.}
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+\title{Finds the effect sizes for all genes in the original dataset, regardless of
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+significance.}
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 \usage{
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 calcEffectSizes(countMatrix, condition)
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 }
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 \arguments{
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 \item{countMatrix}{Matrix. A simulated counts matrix, sans labels.}
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-\item{condition}{Factor. The condition labels for the simulated cells. If more than 2 conditions are given, the first will be compared to all others by default.}
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+\item{condition}{Factor. The condition labels for the simulated cells. If
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+more than 2 conditions are given, the first will be compared to all others by
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+default.}
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 }
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 \value{
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 A vector of cohen's d effect sizes for each gene.
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 }
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 \description{
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-Finds the effect sizes for all genes in the original dataset, regardless of significance.
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+Finds the effect sizes for all genes in the original dataset, regardless of
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+significance.
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 }
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ran devtools::document()

David Jenkins authored on 06/11/2017 22:35:53
Showing 1 changed files
man/calcEffectSizes.Rd
History View file @ 40e88096
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new file mode 100644
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@@ -0,0 +1,19 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/Downsample.Matrix.R
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+\name{calcEffectSizes}
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+\alias{calcEffectSizes}
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+\title{Finds the effect sizes for all genes in the original dataset, regardless of significance.}
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+\usage{
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+calcEffectSizes(countMatrix, condition)
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+}
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+\arguments{
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+\item{countMatrix}{Matrix. A simulated counts matrix, sans labels.}
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+
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+\item{condition}{Factor. The condition labels for the simulated cells. If more than 2 conditions are given, the first will be compared to all others by default.}
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+}
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+\value{
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+A vector of cohen's d effect sizes for each gene.
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+}
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+\description{
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+Finds the effect sizes for all genes in the original dataset, regardless of significance.
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+}