Missing inferCNV output file in version 1.22.0: HMM_CNV_predictions.HMMi6.rand_trees.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_regions.dat #29
Description
Hi inferCNV Developers,
First, I would like to thank you for developing and maintaining this powerful tool.
I recently ran inferCNV version 1.22, and I noticed that the expected output file: HMM_CNV_predictions.HMMi6.rand_trees.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_regions.dat is not in the out put.
#install latest version of infer CNV
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("infercnv")
infercnv_obj21 = CreateInfercnvObject(raw_counts_matrix=GetAssayData(GSM6710021_obj,"RNA"),
annotations_file=as.matrix(Idents(GSM6710021_obj)),
gene_order_file="E:/Multiple Myeloma project/Copy Number Variation/CNV Multiple Myeloma Samples/hg38_gencode_v27.txt",delim ="\t",
ref_group_names=c("CD8+ T ", "CD4+ T ", "monocytes",
"erythrocytes", "B cells" , "NK", "HSPCs","plasma" )
)
infercnv_obj21 = infercnv::run(infercnv_obj21,cutoff=1,out_dir="output_dir21",cluster_by_groups=FALSE,plot_steps=T,scale_data=T,denoise=T,noise_filter=0.12,analysis_mode='subclusters',HMM_type='i6',num_threads=1)
Questions & Request for Clarification
Has the output format changed in inferCNV v1.22?
Is the missing file generated under a different versions?
Are there new parameters required to produce this file?
Any guidance would be greatly appreciated! Thanks again for your work on this tool.