Merge pull request #190 from zhanghao-njmu/develop

remove rliger dependency
zhanghao-njmu · Oct 25, 2023 · 5bd2f72 · 5bd2f72
2 parents 39ff0aa + 11b00e3
commit 5bd2f72
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Showing 3 changed files with 3 additions and 4 deletions.
diff --git 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
@@ -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