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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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The running time #344

Closed zym826 closed 3 years ago

zym826 commented 3 years ago

Hello, I did not report an error when creating the object.It didn't end for a long time, probably several hours.Is this normal? code: infercnv_obj = CreateInfercnvObject(raw_counts_matrix=data, annotations_file="cellAnnotations.txt",delim="\t",gene_order_file="gene.txt", ref_group_names=c("Epithelial(non-malignant)")) infercnv_obj = infercnv::run(infercnv_obj, cutoff=0.1, # use 1 for smart-seq, 0.1 for 10x-genomics out_dir="output_dir", # dir is auto-created for storing outputs cluster_by_groups=T, # cluster denoise=F, HMM=F )

My data have 16000 genes and 25000 cells, is running time related to the amount of data?

zym826 commented 3 years ago

Error in .External2(C_X11, paste0("png::", filename), g$width, g$height, : Unable to open the PNG device In addition: Warning message: In png(paste(out_dir, paste(output_filename, ".png", sep = ""), : Unable to open link to X11 display