Warning message:程辑包‘Seurat’是用R版本4.0.3来建造的>library(ggplot2)>library(infercnv)Warning message:程辑包‘infercnv’是用R版本4.0.3来建造的>expFile='expFile.txt'>groupFiles='groupFiles.txt'>geneFile='geneFile.txt'>infercnv_obj=CreateInfercnvObject(raw_counts_matrix=expFile,+annotations_...
2.inferCNV预测CNV,并依据CNV聚类 这次教程用到的测试数据同上上篇一样,肿瘤细胞来源于4个病人。但是为了演示,我假设这些细胞都来源于一个病人,是不同的亚克隆。 library(infercnv) #1 infercnv_obj = CreateInfercnvObject(raw_counts_matrix="oligodendroglioma_expression_downsampled.counts.matrix", annotations_file=...
should not happen. Error in .plot_cnv_references(infercnv_obj = infercnv_obj, ref_data = ref_data_t,: Error Calls: <Anonymous> -> plot_cnv -> .plot_cnv_references 5: (function () traceback(2))() 4: stop("Error") 3: .plot_cnv_references(infercnv_obj = infercnv_obj, ref_data...
INFO [2023-06-16 13:38:19] plot_cnv(): auto thresholding at: (NA , NA) Error in seq.default(x.range[1], x.range[2], length.out = nb_breaks) : 'from' must be a finite number infercnvobj An object of class "infercnv" Slot "expr.data": 32480 x 25542 sparse Matrix of class...
要生成必要的文件,inferCNV 需要与 HMM 一起运行,并将cluster_by_groups设置为FALSE, 以及analysis_mode="subclusters",这将生成用于绘图的“HMM_CNV_predictions.HMMi6.rand_trees.hmm_mode-subclusters.Pnorm_0.5.cell_groupings”等文件 infercnv_obj=infercnv::run(infercnv_obj,cutoff=1,out_dir="output_dir...
2. inferCNV预测CNV,并依据CNV聚类 这次教程用到的测试数据同上上篇一样,肿瘤细胞来源于4个病人。但是为了演示,我假设这些细胞都来源于一个病人,是不同的亚克隆。 library(infercnv)#1infercnv_obj=CreateInfercnvObject(raw_counts_matrix="oligodendroglioma_expression_downsampled.counts.matrix",annotations_file="oligo...
Hi, Is there a way to keep the sample names in the rows of the output CNV plot? For e.g. here the rows don't have any annotation so I can't figure out which row belongs to what sample. infercnv.pdf Thanks Komal``Collaborator GeorgescuC commented Aug 14, 2018 Hi @komalsrathi ...