diff --git a/DESCRIPTION b/DESCRIPTION index f6fae51b..9c67e018 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -95,7 +95,6 @@ Suggests: ragg, reactome.db, renv, - rliger, RcppParallel, RcppML, scattermore, diff --git a/R/SCP-cellqc.R b/R/SCP-cellqc.R index a8701232..8287e678 100644 --- a/R/SCP-cellqc.R +++ b/R/SCP-cellqc.R @@ -258,7 +258,7 @@ isOutlier <- function(x, nmads = 2.5, constant = 1.4826, type = c("both", "lower #' This function handles multiple quality control methods for single-cell RNA-seq data. #' #' @inheritParams RunDoubletCalling -#' @param batch Name of the batch variable to split the Seurat object. Default is NULL. +#' @param split.by Name of the sample variable to split the Seurat object. Default is NULL. #' @param qc_metrics A character vector specifying the quality control metrics to be applied. Default is #' `c("doublets", "outlier", "umi", "gene", "mito", "ribo", "ribo_mito_ratio", "species")`. #' @param return_filtered Logical indicating whether to return a cell-filtered Seurat object. Default is FALSE. diff --git a/man/RunCellQC.Rd b/man/RunCellQC.Rd index 29f91753..e239d7ed 100644 --- a/man/RunCellQC.Rd +++ b/man/RunCellQC.Rd @@ -38,6 +38,8 @@ RunCellQC( \item{assay}{The name of the assay to be used for doublet-calling. Default is "RNA".} +\item{split.by}{Name of the sample variable to split the Seurat object. Default is NULL.} + \item{qc_metrics}{A character vector specifying the quality control metrics to be applied. Default is `c("doublets", "outlier", "umi", "gene", "mito", "ribo", "ribo_mito_ratio", "species")`.} @@ -79,8 +81,6 @@ RunCellQC( \item{species_percent}{Percentage of UMI counts of the first species. Cells that exceed this threshold will be considered as kept. Default is 95.} \item{seed}{Set a random seed. Default is 11.} - -\item{batch}{Name of the batch variable to split the Seurat object. Default is NULL.} } \value{ Returns Seurat object with the QC results stored in the meta.data slot.