Dear team,
Thanks for the great package!
I ran my scRNA-seq successfully, but failed to find the infercnv.observations_dendrogram.txt
The lattest file were listed as follows:
This is the script:
scRNA2[["celltype"]] <- "nomal_cell"
scRNA3[["celltype"]] <- "Malignant_N2"
DefaultAssay(scRNA2) <- "RNA"
DefaultAssay(scRNA3) <- "RNA"
cnvtest <- merge(scRNA2, scRNA3, project = "cnvtest")
counts_matrix <- cnvtest@assays$RNA@counts
cellannotation <- cnvtest@meta.data$celltype
cellannotation <- as.data.frame(cellannotation)
Dear team, Thanks for the great package! I ran my scRNA-seq successfully, but failed to find the infercnv.observations_dendrogram.txt The lattest file were listed as follows:
This is the script:
scRNA2[["celltype"]] <- "nomal_cell"
scRNA3[["celltype"]] <- "Malignant_N2"
DefaultAssay(scRNA2) <- "RNA"
DefaultAssay(scRNA3) <- "RNA"
cnvtest <- merge(scRNA2, scRNA3, project = "cnvtest")
counts_matrix <- cnvtest@assays$RNA@counts
cellannotation <- cnvtest@meta.data$celltype
cellannotation <- as.data.frame(cellannotation)
rownames(cellannotation) <- colnames(cnvtest@assays$RNA@counts) refgenes <- read.table("gencode_v19_gene_pos.txt", header = F, row.names = 1) infercnv_obj <- CreateInfercnvObject(raw_counts_matrix = counts_matrix, annotations_file = cellannotation, delim = "\t", gene_order_file = refgenes, ref_group_names = c("nomal_cell")) infercnv_obj = infercnv::run(infercnv_obj, cutoff=0.1,
out_dir="ceshi/",
cluster_by_groups=T,
denoise=F, HMM=F, write_expr_matrix=TRUE, leiden_resolution=0.0005, k_obs_groups=8 )