From 5603599de5bc299d3f5fa79ab4ca64d50af13da6 Mon Sep 17 00:00:00 2001 From: LTLA Date: Tue, 13 Feb 2024 23:14:48 -0800 Subject: [PATCH] Minor docfixes, mostly related to the absence of first.labels. --- DESCRIPTION | 6 +++--- R/combineCommonResults.R | 2 +- R/pruneScores.R | 2 +- man/combineCommonResults.Rd | 2 +- man/pruneScores.Rd | 2 +- vignettes/SingleR.Rmd | 2 +- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c35d41e..2773d28 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: SingleR Title: Reference-Based Single-Cell RNA-Seq Annotation -Version: 2.5.1 -Date: 2024-01-05 +Version: 2.5.2 +Date: 2024-02-13 Authors@R: c(person("Dvir", "Aran", email="dvir.aran@ucsf.edu", role=c("aut", "cph")), person("Aaron", "Lun", email="infinite.monkeys.with.keyboards@gmail.com", role=c("ctb", "cre")), person("Daniel", "Bunis", role="ctb"), @@ -57,6 +57,6 @@ biocViews: SystemRequirements: C++17 VignetteBuilder: knitr Encoding: UTF-8 -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 URL: https://github.com/LTLA/SingleR BugReports: https://support.bioconductor.org/ diff --git a/R/combineCommonResults.R b/R/combineCommonResults.R index 9a1ce40..34eac20 100644 --- a/R/combineCommonResults.R +++ b/R/combineCommonResults.R @@ -13,7 +13,7 @@ #' \item \code{references}, an integer vector specifying the reference from which the combined label was derived. #' \item \code{orig.results}, a DataFrame containing \code{results}. #' } -#' It may also contain \code{first.labels} and \code{pruned.labels} if these were also present in \code{results}. +#' It may also contain \code{pruned.labels} if these were also present in \code{results}. #' #' The \code{\link{metadata}} contains \code{common.genes}, #' a character vector of the common genes that were used across all references in \code{results}; diff --git a/R/pruneScores.R b/R/pruneScores.R index 812fd40..c26b0e5 100644 --- a/R/pruneScores.R +++ b/R/pruneScores.R @@ -19,7 +19,7 @@ #' resulting in assignment of an incorrect label to that cell. #' The \code{pruneScores} function aims to mitigate this effect by removing poor-quality assignments with \dQuote{low} scores. #' -#' We compute a \dQuote{delta} value for each cell, defined as the difference between the score for the assigned label and the and median score across all labels. +#' We compute a \dQuote{delta} value for each cell, defined as the difference between the score for the assigned label and the median score across all labels. #' If the delta is small, this indicates that the cell matches all labels with the same confidence such that the assigned label is not particularly meaningful. #' The aim is to discard low delta values caused by (i) ambiguous assignments with closely related reference labels and (ii) incorrect assignments that match poorly to all reference labels. #' diff --git a/man/combineCommonResults.Rd b/man/combineCommonResults.Rd index 79e5d77..4739a32 100644 --- a/man/combineCommonResults.Rd +++ b/man/combineCommonResults.Rd @@ -18,7 +18,7 @@ This mimics the output of \code{\link{classifySingleR}} and contains the followi \item \code{references}, an integer vector specifying the reference from which the combined label was derived. \item \code{orig.results}, a DataFrame containing \code{results}. } -It may also contain \code{first.labels} and \code{pruned.labels} if these were also present in \code{results}. +It may also contain \code{pruned.labels} if these were also present in \code{results}. The \code{\link{metadata}} contains \code{common.genes}, a character vector of the common genes that were used across all references in \code{results}; diff --git a/man/pruneScores.Rd b/man/pruneScores.Rd index e163765..00cca22 100644 --- a/man/pruneScores.Rd +++ b/man/pruneScores.Rd @@ -37,7 +37,7 @@ This occurs even if the cell's true label is not represented in the reference se resulting in assignment of an incorrect label to that cell. The \code{pruneScores} function aims to mitigate this effect by removing poor-quality assignments with \dQuote{low} scores. -We compute a \dQuote{delta} value for each cell, defined as the difference between the score for the assigned label and the and median score across all labels. +We compute a \dQuote{delta} value for each cell, defined as the difference between the score for the assigned label and the median score across all labels. If the delta is small, this indicates that the cell matches all labels with the same confidence such that the assigned label is not particularly meaningful. The aim is to discard low delta values caused by (i) ambiguous assignments with closely related reference labels and (ii) incorrect assignments that match poorly to all reference labels. diff --git a/vignettes/SingleR.Rmd b/vignettes/SingleR.Rmd index 37ef78f..eaf1ee8 100644 --- a/vignettes/SingleR.Rmd +++ b/vignettes/SingleR.Rmd @@ -74,7 +74,7 @@ pred.hesc <- SingleR(test = hESCs, ref = hpca.se, assay.type.test=1, ``` Each row of the output `DataFrame` contains prediction results for a single cell. -Labels are shown before fine-tuning (`first.labels`), after fine-tuning (`labels`) and after pruning (`pruned.labels`), along with the associated scores. +Labels are shown before (`labels`) and after pruning (`pruned.labels`), along with the associated scores. ```{r} pred.hesc