subset() 取Seurat的子集,很常见,其subset参数十分强大,遗憾的是我对R中的表达式类型不是很懂,该部分的源码也遇到理解障碍。先标记上,以后再说吧。//todo # $ find . | grep "R$" | xargs grep -n "subset" --color=auto # seurat-object-4.0.4/R/seurat.R:2497:subset.Seurat <- function( # seu...
Hi, I'm having trouble subsetting a Seurat object in v3. I get the following error but don't understand where it's coming from: > cells <- sample(Neocortex@meta.data %>% rownames, 10000) > neocortex.small <- SubsetData(object = Neocortex...
(x=scRNA,subset=nFeatures>500&PC1>5,idents="B cells")subset(x=scRNA,subset=orig.ident=="Replicate1")subset(x=scRNA,downsample=100)subset(x=scRNA,features=VariableFeatures(object=scRNA))scRNA=scRNA[,scRNA@meta.data$seurat_clusters%in%c(0,2)]scRNA=scRNA[,Idents(scRNA)%in%c("T cell","B...
stop("Only Seurat object is supported") }if (length(feature) == 1) { res <- subset_cell_internal(x, feature, method = method, n) return(x[, res$idx]) }if (length(n) == 1) n <- rep(n, length(feature)) res <- lapply(seq_along(feature), function(i) { subset_cell_interna...
TFCs clusters and accompanying nonnormalized gene expression count data from the final integrated Seurat object were used as inputs to create Monocle v2 newCellDataSet31,56. Differential expression between clusters was calculated using differentialGeneTest function in Monocle. DDRTree method was used for...
Returns a subsetted Motif object See Also subset Examples motif.obj <- Seurat::GetAssayData( object = atac_small[['peaks']], slot = "motifs" ) subset(x = motif.obj, features = head(rownames(motif.obj), 10)) motif.obj <- Seurat::GetAssayData( object = atac_small, assay = '...
Seurat::subset() doesn't accept soft-coded parameters inside a function. I'm attempting to deliver a Seurat pipeline via a Java web-server so I would like to create a function that allows the user to make choices on normalizing/scaling t...
(R 4.2.0) Seurat * 4.3.0.1 2023-06-22 [1] CRAN (R 4.2.0) SeuratObject * 4.1.3 2022-11-07 [1] CRAN (R 4.2.0) shape 1.4.6 2021-05-19 [1] CRAN (R 4.2.0) shiny 1.7.5 2023-08-12 [1] CRAN (R 4.2.0) SingleCellExperiment * 1.20.1 2023-03-19 [1] Bioconductor sn ...
[19] sp_1.5-0 SeuratObject_4.1.0 [21] Seurat_4.1.1 loaded via a namespace (and not attached): [1] uuid_1.1-0 plyr_1.8.7 [3] igraph_1.3.2 repr_1.1.4 [5] lazyeval_0.2.2 splines_4.0.1 [7] BiocParallel_1.24.1 listenv_0.8.0 [9] scattermore_0.8 digest_0.6.29 [11] htmltoo...