上周运行成功的代码如下:
infercnv_obj = CreateInfercnvObject(raw_counts_matrix="counts.matrix.txt.gz",
annotations_file="Cell_type.txt",
delim="\t",
gene_order_file="hg38_gencode_v27.txt",
ref_group_names = c("Myeloid cells",
infercnv_obj = readRDS(file = "../14_invert_log_transformHMMi6.infercnv_obj")
# 运行inferCNV程序
infercnv_obj = infercnv::run(infercnv_obj,
cutoff=0.1, # cutoff=1 works well for Smartseq2,and cutoff=0.1 works well for 10x Genomics
out_dir="./",
cluster_by_groups=TRUE,
denoise=TRUE,
HMM=TRUE,num_threads = 40)
再次运行后报错如下:
STEP 15: computing tumor subclusters via leiden
INFO [2023-09-11 08:22:45] define_signif_tumor_subclusters(p_val=0.1
INFO [2023-09-11 08:22:45] define_signif_tumor_subclusters(), tumor: 0
Counts matrix provided is not sparse. Creating V5 assay in Seurat Object.
Error in GetAssay.Seurat(object = object, assay = assay) :
infercnv is not an assay present in the given object. Available assays are:
以上为完整报错,第15步出现上述报错,请是什么原因呢? 该怎么解决呢?