From 97d7e3af04a57e9b1abbe226592938726e8bf161 Mon Sep 17 00:00:00 2001 From: Jack Leary Date: Wed, 16 Oct 2024 11:01:23 -0400 Subject: [PATCH] minor doc change --- R/getFittedValues.R | 4 ++-- man/getFittedValues.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/getFittedValues.R b/R/getFittedValues.R index 1a3a1af..dda1285 100644 --- a/R/getFittedValues.R +++ b/R/getFittedValues.R @@ -10,14 +10,14 @@ #' @param test.dyn.res The output from \code{\link{testDynamic}}. Defaults to NULL. #' @param genes A character vector of genes to generate fitted values for. Defaults to NULL. #' @param pt A data.frame of pseudotime values for each cell. Defaults to NULL. -#' @param expr.mat Either a \code{SingleCellExperiment} or \code{Seurat} object from which counts can be extracted, or a matrix of integer-valued counts with genes as rows & cells as columns. Defaults to NULL. +#' @param expr.mat Either a \code{SingleCellExperiment}, \code{Seurat}, or \code{cell_data_set} object from which counts can be extracted, or a matrix of integer-valued counts with genes as rows & cells as columns. Defaults to NULL. #' @param size.factor.offset (Optional) An offset to be used to rescale the fitted values. Can be generated easily with \code{\link{createCellOffset}}. No need to provide if the GEE backend was used. Defaults to NULL. #' @param log1p.norm (Optional) Should log1p-normalized versions of expression & model predictions be returned as well? Defaults to TRUE. #' @param cell.meta.data (Optional) A data.frame of metadata values for each cell (celltype label, subject characteristics, tissue type, etc.) that will be included in the result table. Defaults to NULL. #' @param is.gee Was the GEE mode used to fit the models? Defaults to FALSE. #' @param id.vec (Optional) A vector of subject IDs used in fitting GEE or GLMM models. Defaults to NULL. #' @param ci.alpha (Optional) The pre-specified Type I Error rate used in generating (\eqn{1 - \alpha})\% CIs. Defaults to good old 0.05. -#' @param filter.lineage (Optional) A character vector of lineages to filter out before generating the final plot. Should be letters, i.e. lineage "A" or "B". Defaults to NULL. +#' @param filter.lineage (Optional) A character vector of lineages to filter out. Should be letters, i.e. lineage "A" or "B". Defaults to NULL. #' @return A data.frame containing depth- and log1p-normalized expression, model predictions, and cell-level metadata. #' @export #' @examples diff --git a/man/getFittedValues.Rd b/man/getFittedValues.Rd index 0ddf96d..8ef6928 100644 --- a/man/getFittedValues.Rd +++ b/man/getFittedValues.Rd @@ -25,7 +25,7 @@ getFittedValues( \item{pt}{A data.frame of pseudotime values for each cell. Defaults to NULL.} -\item{expr.mat}{Either a \code{SingleCellExperiment} or \code{Seurat} object from which counts can be extracted, or a matrix of integer-valued counts with genes as rows & cells as columns. Defaults to NULL.} +\item{expr.mat}{Either a \code{SingleCellExperiment}, \code{Seurat}, or \code{cell_data_set} object from which counts can be extracted, or a matrix of integer-valued counts with genes as rows & cells as columns. Defaults to NULL.} \item{size.factor.offset}{(Optional) An offset to be used to rescale the fitted values. Can be generated easily with \code{\link{createCellOffset}}. No need to provide if the GEE backend was used. Defaults to NULL.} @@ -39,7 +39,7 @@ getFittedValues( \item{ci.alpha}{(Optional) The pre-specified Type I Error rate used in generating (\eqn{1 - \alpha})\% CIs. Defaults to good old 0.05.} -\item{filter.lineage}{(Optional) A character vector of lineages to filter out before generating the final plot. Should be letters, i.e. lineage "A" or "B". Defaults to NULL.} +\item{filter.lineage}{(Optional) A character vector of lineages to filter out. Should be letters, i.e. lineage "A" or "B". Defaults to NULL.} } \value{ A data.frame containing depth- and log1p-normalized expression, model predictions, and cell-level metadata.