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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Infercnv.observations_Dendrogram.txt #592

Open zhongguozhiwang opened 10 months ago

zhongguozhiwang commented 10 months ago

May I ask why there is no Infercnv.observations_Dendrogram.txt result file after running infercnv?

infercnv_obj = infercnv::run(infercnv_obj, # inferCNV对象
                                 cutoff = 0.1, # use 1 for smart-seq, 0.1 for 10x-genomics
                                 out_dir = "result/", 
                                 cluster_by_groups = TRUE, # cluster_by_groups：先区分细胞来源，再做层次聚类
                                 HMM = FALSE,
                                 denoise = TRUE,
                                 hclust_method="ward.D2", plot_steps=F,
                                 write_expr_matrix=TRUE,
                                 num_threads = 8)

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dingyaozhang commented 10 months ago

I think you could add "write_phylo = TRUE"

zhongguozhiwang commented 10 months ago

Ok, thank you.