How might I add the ambiguous, matrix, spliced, unspliced to my Seurat GEX cluster object? Do I do as below? test[["ambiguous"]] <- CreateAssayObject(counts = concat_adata_Seurat@assays$ambiguous) test[["matrix"]] <- CreateAssayObject(counts = concat_adata_Seurat@assays$matrix) ...
function (object, features, pool = NULL, nbin = 24, ctrl = 100, k = FALSE, assay = NULL, name = "Cluster", seed = 1, search = FALSE, ...) { if (!is.null(x = seed)) { set.seed(seed = seed) } assay.old <- DefaultAssay(object = object) assay <- assay %||% assay....
Usage: AddModuleScore( object, features, pool = NULL, nbin = 24, ctrl = 100, k = FALSE, assay = NULL, name = "Cluster", seed = 1, search = FALSE, ... ) Arguments: object: Seurat object features: Feature expression programs in list pool: List of features to check expression leve...
I notice that when harmony is used to generate the integrated reference object, then harmony reduction in the integrated reference object fails in Seurat mapping framework. satijalab/seurat#5122 satijalab/seurat#5222 The main reason is that the feature loadings in the harmony reduction is not an ...
An object of class Seurat 3000 features across 59824 samples within 1 assay Active assay: integrated (3000 features) 2 dimensional reductions calculated: pca, umap moe[['integrated']] Assay data with 3000 features for 59824 cells Top 10 variable features: ...
Hi Tim, when trying to build a motif matrix using macaca <- AddMotifs( object = macaca, genome = BSgenome.Mfascicularis.NCBI.5.0.renamed, pfm = pfm ) I get the following error: Error in loadFUN(x, seqname, ranges): trying to load regions...
I haven't look very carefully what would be the best way to resolve it, but as it stands, I have to trim features out from the seurat object to run this function. And as a side note, the pbmc_small appears to have no genes related to the cc.genes data (too small) such that the...
<-FindVariableFeatures(object=subRNA,nfeatures=nGenes,verbose=FALSE DragonlongzhilincommentedMay 12, 2021• edited I am sorry for my irregular operation. Indeed as you said, > Seurat::FindVariableFeatures(seRNA) Error: SCT assay is comprised of multiple SCT models. To change the variable featu...
#' Easy to calculate the hub gene of the geneset based on the correlation between #' the geneset's score and the expression or rank of gene included in the geneset #' #' @param object A Seurat after perform \code{\link{irGSEA.score}} #' @param assay Name of assay to calculate ...