inferCNV测试安装

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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测试安装

infercnv_obj = CreateInfercnvObject(raw_counts_matrix=system.file("extdata", "oligodendroglioma_expression_downsampled.counts.matrix.gz", package = "infercnv"),
+                                     annotations_file=system.file("extdata", "oligodendroglioma_annotations_downsampled.txt", package = "infercnv"),
+                                     delim="\t",
+                                     gene_order_file=system.file("extdata", "gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt", package = "infercnv"),
+                                     ref_group_names=c("Microglia/Macrophage","Oligodendrocytes (non-malignant)"))

INFO [2020-07-06 12:40:59] Parsing matrix: C:/Users/wlx/Documents/R/win-library/3.6/infercnv/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz
INFO [2020-07-06 12:41:02] Parsing gene order file: C:/Users/wlx/Documents/R/win-library/3.6/infercnv/extdata/gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt
INFO [2020-07-06 12:41:02] Parsing cell annotations file: C:/Users/wlx/Documents/R/win-library/3.6/infercnv/extdata/oligodendroglioma_annotations_downsampled.txt
INFO [2020-07-06 12:41:03] ::order_reduce:Start.
INFO [2020-07-06 12:41:03] .order_reduce(): expr and order match.
INFO [2020-07-06 12:41:03] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10338,184 Total=18322440.6799817 Min=0 Max=34215.
INFO [2020-07-06 12:41:03] num genes removed taking into account provided gene ordering list: 399 = 3.8595473012188% removed.
INFO [2020-07-06 12:41:03] validating infercnv_obj

infercnv_obj = infercnv::run(infercnv_obj,
+                              cutoff=1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
+                              out_dir=tempfile(), 
+                              cluster_by_groups=TRUE, 
+                              denoise=TRUE,
+                              HMM=TRUE)

INFO [2020-07-06 12:41:03] ::process_data:Start
INFO [2020-07-06 12:41:03] Creating output path C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab
INFO [2020-07-06 12:41:03] Checking for saved results.
INFO [2020-07-06 12:41:03]

STEP 1: incoming data

INFO [2020-07-06 12:41:05]

STEP 02: Removing lowly expressed genes

INFO [2020-07-06 12:41:05] ::above_min_mean_expr_cutoff:Start
INFO [2020-07-06 12:41:05] Removing 1431 genes from matrix as below mean expr threshold: 1
INFO [2020-07-06 12:41:05] validating infercnv_obj
INFO [2020-07-06 12:41:05] There are 8508 genes and 184 cells remaining in the expr matrix.
INFO [2020-07-06 12:41:05] no genes removed due to min cells/gene filter
INFO [2020-07-06 12:41:06]

STEP 03: normalization by sequencing depth

INFO [2020-07-06 12:41:06] normalizing counts matrix by depth
INFO [2020-07-06 12:41:07] Computed total sum normalization factor as median libsize: 93909.929740
INFO [2020-07-06 12:41:07] Adding h-spike
INFO [2020-07-06 12:41:07] -hspike modeling of Microglia/Macrophage
INFO [2020-07-06 12:43:39] -hspike modeling of Oligodendrocytes (non-malignant)
INFO [2020-07-06 12:45:59] validating infercnv_obj
INFO [2020-07-06 12:45:59] normalizing counts matrix by depth
INFO [2020-07-06 12:46:00] Using specified normalization factor: 93909.929740
INFO [2020-07-06 12:46:04]

STEP 04: log transformation of data

INFO [2020-07-06 12:46:04] transforming log2xplus1()
INFO [2020-07-06 12:46:04] -mirroring for hspike
INFO [2020-07-06 12:46:04] transforming log2xplus1()
INFO [2020-07-06 12:46:09]

STEP 08: removing average of reference data (before smoothing)

INFO [2020-07-06 12:46:09] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-07-06 12:46:09] subtracting mean(normal) per gene per cell across all data
INFO [2020-07-06 12:46:14] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-07-06 12:46:15] -mirroring for hspike
INFO [2020-07-06 12:46:15] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-07-06 12:46:15] subtracting mean(normal) per gene per cell across all data
INFO [2020-07-06 12:46:20] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-07-06 12:46:26]

STEP 09: apply max centered expression threshold: 3

INFO [2020-07-06 12:46:26] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2020-07-06 12:46:26] -mirroring for hspike
INFO [2020-07-06 12:46:26] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2020-07-06 12:46:32]

STEP 10: Smoothing data per cell by chromosome

INFO [2020-07-06 12:46:32] smooth_by_chromosome: chr: chr1
INFO [2020-07-06 12:46:32] smooth_by_chromosome: chr: chr2
INFO [2020-07-06 12:46:32] smooth_by_chromosome: chr: chr3
INFO [2020-07-06 12:46:33] smooth_by_chromosome: chr: chr4
INFO [2020-07-06 12:46:33] smooth_by_chromosome: chr: chr5
INFO [2020-07-06 12:46:34] smooth_by_chromosome: chr: chr6
INFO [2020-07-06 12:46:34] smooth_by_chromosome: chr: chr7
INFO [2020-07-06 12:46:34] smooth_by_chromosome: chr: chr8
INFO [2020-07-06 12:46:34] smooth_by_chromosome: chr: chr9
INFO [2020-07-06 12:46:35] smooth_by_chromosome: chr: chr10
INFO [2020-07-06 12:46:35] smooth_by_chromosome: chr: chr11
INFO [2020-07-06 12:46:35] smooth_by_chromosome: chr: chr12
INFO [2020-07-06 12:46:36] smooth_by_chromosome: chr: chr13
INFO [2020-07-06 12:46:36] smooth_by_chromosome: chr: chr14
INFO [2020-07-06 12:46:36] smooth_by_chromosome: chr: chr15
INFO [2020-07-06 12:46:37] smooth_by_chromosome: chr: chr16
INFO [2020-07-06 12:46:37] smooth_by_chromosome: chr: chr17
INFO [2020-07-06 12:46:37] smooth_by_chromosome: chr: chr18
INFO [2020-07-06 12:46:37] smooth_by_chromosome: chr: chr19
INFO [2020-07-06 12:46:38] smooth_by_chromosome: chr: chr20
INFO [2020-07-06 12:46:38] smooth_by_chromosome: chr: chr21
INFO [2020-07-06 12:46:38] smooth_by_chromosome: chr: chr22
INFO [2020-07-06 12:46:39] -mirroring for hspike
INFO [2020-07-06 12:46:39] smooth_by_chromosome: chr: chrA
INFO [2020-07-06 12:46:40] smooth_by_chromosome: chr: chr_0
INFO [2020-07-06 12:46:40] smooth_by_chromosome: chr: chr_B
INFO [2020-07-06 12:46:41] smooth_by_chromosome: chr: chr_0pt5
INFO [2020-07-06 12:46:42] smooth_by_chromosome: chr: chr_C
INFO [2020-07-06 12:46:42] smooth_by_chromosome: chr: chr_1pt5
INFO [2020-07-06 12:46:43] smooth_by_chromosome: chr: chr_D
INFO [2020-07-06 12:46:44] smooth_by_chromosome: chr: chr_2pt0
INFO [2020-07-06 12:46:44] smooth_by_chromosome: chr: chr_E
INFO [2020-07-06 12:46:45] smooth_by_chromosome: chr: chr_3pt0
INFO [2020-07-06 12:46:46] smooth_by_chromosome: chr: chr_F
INFO [2020-07-06 12:46:54]

STEP 11: re-centering data across chromosome after smoothing

INFO [2020-07-06 12:46:54] ::center_smooth across chromosomes per cell
INFO [2020-07-06 12:46:54] -mirroring for hspike
INFO [2020-07-06 12:46:54] ::center_smooth across chromosomes per cell
INFO [2020-07-06 12:47:01]

STEP 12: removing average of reference data (after smoothing)

INFO [2020-07-06 12:47:01] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-07-06 12:47:01] subtracting mean(normal) per gene per cell across all data
INFO [2020-07-06 12:47:06] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-07-06 12:47:07] -mirroring for hspike
INFO [2020-07-06 12:47:07] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2020-07-06 12:47:07] subtracting mean(normal) per gene per cell across all data
INFO [2020-07-06 12:47:15] -subtracting expr per gene, use_bounds=TRUE
INFO [2020-07-06 12:47:23]

STEP 14: invert log2(FC) to FC

INFO [2020-07-06 12:47:23] invert_log2(), computing 2^x
INFO [2020-07-06 12:47:23] -mirroring for hspike
INFO [2020-07-06 12:47:23] invert_log2(), computing 2^x
INFO [2020-07-06 12:47:30]

STEP 15: Clustering samples (not defining tumor subclusters)

INFO [2020-07-06 12:47:30] define_signif_tumor_subclusters(p_val=0.1
INFO [2020-07-06 12:47:30] define_signif_tumor_subclusters(), tumor: malignant_MGH36
INFO [2020-07-06 12:47:30] cut tree into: 1 groups
INFO [2020-07-06 12:47:30] -processing malignant_MGH36,malignant_MGH36_s1
INFO [2020-07-06 12:47:30] define_signif_tumor_subclusters(), tumor: malignant_MGH53
INFO [2020-07-06 12:47:30] cut tree into: 1 groups
INFO [2020-07-06 12:47:30] -processing malignant_MGH53,malignant_MGH53_s1
INFO [2020-07-06 12:47:30] define_signif_tumor_subclusters(), tumor: malignant_93
INFO [2020-07-06 12:47:31] cut tree into: 1 groups
INFO [2020-07-06 12:47:31] -processing malignant_93,malignant_93_s1
INFO [2020-07-06 12:47:31] define_signif_tumor_subclusters(), tumor: malignant_97
INFO [2020-07-06 12:47:31] cut tree into: 1 groups
INFO [2020-07-06 12:47:31] -processing malignant_97,malignant_97_s1
INFO [2020-07-06 12:47:31] define_signif_tumor_subclusters(), tumor: Microglia/Macrophage
INFO [2020-07-06 12:47:31] cut tree into: 1 groups
INFO [2020-07-06 12:47:31] -processing Microglia/Macrophage,Microglia/Macrophage_s1
INFO [2020-07-06 12:47:31] define_signif_tumor_subclusters(), tumor: Oligodendrocytes (non-malignant)
INFO [2020-07-06 12:47:31] cut tree into: 1 groups
INFO [2020-07-06 12:47:31] -processing Oligodendrocytes (non-malignant),Oligodendrocytes (non-malignant)_s1
INFO [2020-07-06 12:47:31] -mirroring for hspike
INFO [2020-07-06 12:47:31] define_signif_tumor_subclusters(p_val=0.1
INFO [2020-07-06 12:47:31] define_signif_tumor_subclusters(), tumor: spike_tumor_cell_Microglia/Macrophage
INFO [2020-07-06 12:47:32] cut tree into: 1 groups
INFO [2020-07-06 12:47:32] -processing spike_tumor_cell_Microglia/Macrophage,spike_tumor_cell_Microglia/Macrophage_s1
INFO [2020-07-06 12:47:32] define_signif_tumor_subclusters(), tumor: spike_tumor_cell_Oligodendrocytes (non-malignant)
INFO [2020-07-06 12:47:32] cut tree into: 1 groups
INFO [2020-07-06 12:47:32] -processing spike_tumor_cell_Oligodendrocytes (non-malignant),spike_tumor_cell_Oligodendrocytes (non-malignant)_s1
INFO [2020-07-06 12:47:32] define_signif_tumor_subclusters(), tumor: simnorm_cell_Microglia/Macrophage
INFO [2020-07-06 12:47:33] cut tree into: 1 groups
INFO [2020-07-06 12:47:33] -processing simnorm_cell_Microglia/Macrophage,simnorm_cell_Microglia/Macrophage_s1
INFO [2020-07-06 12:47:33] define_signif_tumor_subclusters(), tumor: simnorm_cell_Oligodendrocytes (non-malignant)
INFO [2020-07-06 12:47:33] cut tree into: 1 groups
INFO [2020-07-06 12:47:33] -processing simnorm_cell_Oligodendrocytes (non-malignant),simnorm_cell_Oligodendrocytes (non-malignant)_s1
INFO [2020-07-06 12:47:43] ::plot_cnv:Start
INFO [2020-07-06 12:47:43] ::plot_cnv:Current data dimensions (r,c)=8508,184 Total=1565375.78852005 Min=0.530812412297805 Max=1.98172179650671.
INFO [2020-07-06 12:47:43] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2020-07-06 12:47:49] plot_cnv(): auto thresholding at: (0.649779 , 1.350098)
INFO [2020-07-06 12:47:49] plot_cnv_observation:Start
INFO [2020-07-06 12:47:49] Observation data size: Cells= 142 Genes= 8508
INFO [2020-07-06 12:47:49] clustering observations via method: ward.D
INFO [2020-07-06 12:47:49] plot_cnv_observation:Writing observation groupings/color.
INFO [2020-07-06 12:47:51] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 12:47:51] Quantiles of plotted data range: 0.649778667373698,0.930913786150194,1,1.06475965837873,1.35009841572973
INFO [2020-07-06 12:47:52] plot_cnv_references:Writing observation data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.preliminary.observations.txt
INFO [2020-07-06 12:47:56] plot_cnv_references:Start
INFO [2020-07-06 12:47:56] Reference data size: Cells= 42 Genes= 8508
INFO [2020-07-06 12:47:56] plot_cnv_references:Number reference groups= 2
INFO [2020-07-06 12:47:56] plot_cnv_references:Plotting heatmap.
INFO [2020-07-06 12:47:56] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 12:47:56] Quantiles of plotted data range: 0.693386142642158,0.960381368823128,1,1.04021212541359,1.35009841572973
INFO [2020-07-06 12:47:56] plot_cnv_references:Writing reference data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.preliminary.references.txt
INFO [2020-07-06 12:47:58]

STEP 17: HMM-based CNV prediction

INFO [2020-07-06 12:47:58] predict_CNV_via_HMM_on_whole_tumor_samples
INFO [2020-07-06 12:48:03] -done predicting CNV based on initial tumor subclusters
INFO [2020-07-06 12:48:07] get_predicted_CNV_regions(subcluster)
INFO [2020-07-06 12:48:07] -processing cell_group_name: malignant_MGH36.malignant_MGH36_s1, size: 33
INFO [2020-07-06 12:48:23] -processing cell_group_name: malignant_MGH53.malignant_MGH53_s1, size: 34
INFO [2020-07-06 12:48:39] -processing cell_group_name: malignant_93.malignant_93_s1, size: 40
INFO [2020-07-06 12:48:56] -processing cell_group_name: malignant_97.malignant_97_s1, size: 35
INFO [2020-07-06 12:49:12] -processing cell_group_name: Microglia/Macrophage.Microglia/Macrophage_s1, size: 19
INFO [2020-07-06 12:49:29] -processing cell_group_name: Oligodendrocytes (non-malignant).Oligodendrocytes (non-malignant)_s1, size: 23
INFO [2020-07-06 12:49:46] -writing cell clusters file: C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/17_HMM_predHMMi6.hmm_mode-samples.cell_groupings
INFO [2020-07-06 12:49:46] -writing cnv regions file: C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_regions.dat
INFO [2020-07-06 12:49:46] -writing per-gene cnv report: C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_genes.dat
INFO [2020-07-06 12:49:46] -writing gene ordering info: C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/17_HMM_predHMMi6.hmm_mode-samples.genes_used.dat
INFO [2020-07-06 12:49:47] ::plot_cnv:Start
INFO [2020-07-06 12:49:47] ::plot_cnv:Current data dimensions (r,c)=8508,184 Total=4728807 Min=2 Max=5.
INFO [2020-07-06 12:49:47] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2020-07-06 12:49:50] plot_cnv_observation:Start
INFO [2020-07-06 12:49:50] Observation data size: Cells= 142 Genes= 8508
INFO [2020-07-06 12:49:50] clustering observations via method: ward.D
INFO [2020-07-06 12:49:51] plot_cnv_observation:Writing observation groupings/color.
INFO [2020-07-06 12:49:52] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 12:49:52] Quantiles of plotted data range: 2,3,3,3,5
INFO [2020-07-06 12:49:53] plot_cnv_references:Writing observation data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.17_HMM_predHMMi6.hmm_mode-samples.observations.txt
INFO [2020-07-06 12:49:55] plot_cnv_references:Start
INFO [2020-07-06 12:49:55] Reference data size: Cells= 42 Genes= 8508
INFO [2020-07-06 12:49:55] plot_cnv_references:Number reference groups= 2
INFO [2020-07-06 12:49:55] plot_cnv_references:Plotting heatmap.
INFO [2020-07-06 12:49:55] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 12:49:55] Quantiles of plotted data range: 3,3,3,3,3
INFO [2020-07-06 12:49:55] plot_cnv_references:Writing reference data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.17_HMM_predHMMi6.hmm_mode-samples.references.txt
INFO [2020-07-06 12:49:56]

STEP 18: Run Bayesian Network Model on HMM predicted CNV's 耗时步骤

INFO [2020-07-06 12:49:56] Creating the following Directory: C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/BayesNetOutput.HMMi6.hmm_mode-samples
INFO [2020-07-06 12:49:56] Initializing new MCM InferCNV Object.
INFO [2020-07-06 12:49:56] validating infercnv_obj
INFO [2020-07-06 12:49:57] Total CNV's: 71
INFO [2020-07-06 12:49:57] Loading BUGS Model.
INFO [2020-07-06 12:49:57] Running Sampling Using Parallel with 4 Cores
INFO [2020-07-06 13:17:42] Obtaining probabilities post-sampling
INFO [2020-07-06 13:18:08] Gibbs sampling time: 28.1821531335513 Minutes
INFO [2020-07-06 13:18:15] ::plot_cnv:Start
INFO [2020-07-06 13:18:15] ::plot_cnv:Current data dimensions (r,c)=8508,184 Total=254238.444853449 Min=0 Max=0.978982144750081.
INFO [2020-07-06 13:18:15] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2020-07-06 13:18:15] plot_cnv_observation:Start
INFO [2020-07-06 13:18:15] Observation data size: Cells= 142 Genes= 8508
INFO [2020-07-06 13:18:15] clustering observations via method: ward.D
INFO [2020-07-06 13:18:15] plot_cnv_observation:Writing observation groupings/color.
INFO [2020-07-06 13:18:17] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:18:17] Quantiles of plotted data range: 0,0,0,0.54143892128094,0.978982144750081
INFO [2020-07-06 13:18:17] plot_cnv_references:Writing observation data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.observations.txt
INFO [2020-07-06 13:18:20] plot_cnv_references:Start
INFO [2020-07-06 13:18:20] Reference data size: Cells= 42 Genes= 8508
INFO [2020-07-06 13:18:20] plot_cnv_references:Number reference groups= 2
INFO [2020-07-06 13:18:20] plot_cnv_references:Plotting heatmap.
INFO [2020-07-06 13:18:20] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:18:20] Quantiles of plotted data range: 0,0,0,0,0
INFO [2020-07-06 13:18:20] plot_cnv_references:Writing reference data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.references.txt
INFO [2020-07-06 13:18:27] Attempting to removing CNV(s) with a probability of being normal above 0.5
INFO [2020-07-06 13:18:27] Removing 0 CNV(s) identified by the HMM.
INFO [2020-07-06 13:18:27] Reassigning CNVs based on state probabilities.
INFO [2020-07-06 13:18:27] Changing the following CNV's states assigned by the HMM to the following based on the CNV's state probabilities.
chr1-region_4 : 4 (P= 0.281744751410082 ) -> 3 (P= 0.434896471897635 )
chr3-region_7 : 4 (P= 0.305191356261855 ) -> 3 (P= 0.419547689064118 )
chr11-region_23 : 4 (P= 0.383353448546477 ) -> 3 (P= 0.385842448827578 )
chr14-region_27 : 4 (P= 0.303100064429691 ) -> 3 (P= 0.445069975554558 )
chr15-region_30 : 4 (P= 0.305226901501801 ) -> 3 (P= 0.497500230997099 )
chr19-region_39 : 4 (P= 0.359646631372442 ) -> 3 (P= 0.459870979799105 )
chr20-region_42 : 4 (P= 0.292300105013017 ) -> 3 (P= 0.379133191053912 )
chr3-region_52 : 4 (P= 0.381083972269155 ) -> 3 (P= 0.417062483798916 )
chr5-region_55 : 4 (P= 0.375268536973786 ) -> 3 (P= 0.40007997960345 )
chr7-region_59 : 4 (P= 0.34756673191588 ) -> 3 (P= 0.388154568737292 )
chr15-region_70 : 4 (P= 0.353846162799462 ) -> 3 (P= 0.488970379187799 )
chr22-region_83 : 4 (P= 0.423136359313185 ) -> 3 (P= 0.444789621591409 )
chr12-region_112 : 4 (P= 0.413133425745833 ) -> 3 (P= 0.456095457376409 )
chr16-region_117 : 4 (P= 0.28960269923133 ) -> 3 (P= 0.479119787890806 )
chr20-region_130 : 4 (P= 0.323410163237048 ) -> 3 (P= 0.398299558610456 )
chr2-region_135 : 4 (P= 0.384069703095295 ) -> 3 (P= 0.390154992733906 )
chr2-region_137 : 4 (P= 0.296234150495901 ) -> 3 (P= 0.411734222033986 )
chr3-region_139 : 4 (P= 0.419584257752293 ) -> 3 (P= 0.45856107871906 )
chr16-region_165 : 4 (P= 0.227482462740539 ) -> 3 (P= 0.430936221914204 )
INFO [2020-07-06 13:18:27] Creating Plots for CNV and cell Probabilities.
INFO [2020-07-06 13:19:44] ::plot_cnv:Start
INFO [2020-07-06 13:19:44] ::plot_cnv:Current data dimensions (r,c)=8508,184 Total=254238.444853449 Min=0 Max=0.978982144750081.
INFO [2020-07-06 13:19:44] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2020-07-06 13:19:44] plot_cnv_observation:Start
INFO [2020-07-06 13:19:44] Observation data size: Cells= 142 Genes= 8508
INFO [2020-07-06 13:19:44] clustering observations via method: ward.D
INFO [2020-07-06 13:19:44] plot_cnv_observation:Writing observation groupings/color.
INFO [2020-07-06 13:19:45] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:19:45] Quantiles of plotted data range: 0,0,0,0.54143892128094,0.978982144750081
INFO [2020-07-06 13:19:46] plot_cnv_references:Writing observation data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PostFiltering.observations.txt
INFO [2020-07-06 13:19:48] plot_cnv_references:Start
INFO [2020-07-06 13:19:48] Reference data size: Cells= 42 Genes= 8508
INFO [2020-07-06 13:19:48] plot_cnv_references:Number reference groups= 2
INFO [2020-07-06 13:19:49] plot_cnv_references:Plotting heatmap.
INFO [2020-07-06 13:19:49] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:19:49] Quantiles of plotted data range: 0,0,0,0,0
INFO [2020-07-06 13:19:49] plot_cnv_references:Writing reference data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PostFiltering.references.txt
INFO [2020-07-06 13:19:55] ::plot_cnv:Start
INFO [2020-07-06 13:19:55] ::plot_cnv:Current data dimensions (r,c)=8508,184 Total=4697546 Min=2 Max=5.
INFO [2020-07-06 13:19:55] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2020-07-06 13:19:58] plot_cnv_observation:Start
INFO [2020-07-06 13:19:58] Observation data size: Cells= 142 Genes= 8508
INFO [2020-07-06 13:19:58] clustering observations via method: ward.D
INFO [2020-07-06 13:19:58] plot_cnv_observation:Writing observation groupings/color.
INFO [2020-07-06 13:19:59] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:19:59] Quantiles of plotted data range: 2,3,3,3,5
INFO [2020-07-06 13:20:00] plot_cnv_references:Writing observation data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.18_HMM_pred.Bayes_Net.Pnorm_0.5.observations.txt
INFO [2020-07-06 13:20:02] plot_cnv_references:Start
INFO [2020-07-06 13:20:02] Reference data size: Cells= 42 Genes= 8508
INFO [2020-07-06 13:20:02] plot_cnv_references:Number reference groups= 2
INFO [2020-07-06 13:20:02] plot_cnv_references:Plotting heatmap.
INFO [2020-07-06 13:20:02] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:20:02] Quantiles of plotted data range: 3,3,3,3,3
INFO [2020-07-06 13:20:02] plot_cnv_references:Writing reference data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.18_HMM_pred.Bayes_Net.Pnorm_0.5.references.txt
INFO [2020-07-06 13:20:04]

STEP 19: Converting HMM-based CNV states to repr expr vals

INFO [2020-07-06 13:20:09] ::plot_cnv:Start
INFO [2020-07-06 13:20:09] ::plot_cnv:Current data dimensions (r,c)=8508,184 Total=1566037 Min=0.5 Max=2.
INFO [2020-07-06 13:20:09] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2020-07-06 13:20:12] plot_cnv_observation:Start
INFO [2020-07-06 13:20:12] Observation data size: Cells= 142 Genes= 8508
INFO [2020-07-06 13:20:12] clustering observations via method: ward.D
INFO [2020-07-06 13:20:12] plot_cnv_observation:Writing observation groupings/color.
INFO [2020-07-06 13:20:14] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:20:14] Quantiles of plotted data range: 0.5,1,1,1,2
INFO [2020-07-06 13:20:14] plot_cnv_references:Writing observation data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.19_HMM_predHMMi6.hmm_mode-samples.Pnorm_0.5.repr_intensities.observations.txt
INFO [2020-07-06 13:20:16] plot_cnv_references:Start
INFO [2020-07-06 13:20:16] Reference data size: Cells= 42 Genes= 8508
INFO [2020-07-06 13:20:16] plot_cnv_references:Number reference groups= 2
INFO [2020-07-06 13:20:16] plot_cnv_references:Plotting heatmap.
INFO [2020-07-06 13:20:17] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:20:17] Quantiles of plotted data range: 1,1,1,1,1
INFO [2020-07-06 13:20:17] plot_cnv_references:Writing reference data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.19_HMM_predHMMi6.hmm_mode-samples.Pnorm_0.5.repr_intensities.references.txt
INFO [2020-07-06 13:20:18]

STEP 21: Denoising

INFO [2020-07-06 13:20:18] ::process_data:Remove noise, noise threshold defined via ref mean sd_amplifier: 1.5
INFO [2020-07-06 13:20:18] denoising using mean(normal) +- sd_amplifier * sd(normal) per gene per cell across all data
INFO [2020-07-06 13:20:18] :: **** clear_noise_via_ref_quantiles **** : removing noise between bounds: 0.886597398348459 - 1.12128464942808
INFO [2020-07-06 13:20:23] ::plot_cnv:Start
INFO [2020-07-06 13:20:23] ::plot_cnv:Current data dimensions (r,c)=8508,184 Total=1569112.28502327 Min=0.530812412297805 Max=1.98172179650671.
INFO [2020-07-06 13:20:23] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2020-07-06 13:20:28] plot_cnv(): auto thresholding at: (0.654552 , 1.350098)
INFO [2020-07-06 13:20:28] plot_cnv_observation:Start
INFO [2020-07-06 13:20:28] Observation data size: Cells= 142 Genes= 8508
INFO [2020-07-06 13:20:28] clustering observations via method: ward.D
INFO [2020-07-06 13:20:28] plot_cnv_observation:Writing observation groupings/color.
INFO [2020-07-06 13:20:30] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:20:30] Quantiles of plotted data range: 0.654552303060852,1.00394102388827,1.00394102388827,1.00394102388827,1.35009841572973
INFO [2020-07-06 13:20:30] plot_cnv_references:Writing observation data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.21_denoised.observations.txt
INFO [2020-07-06 13:20:35] plot_cnv_references:Start
INFO [2020-07-06 13:20:35] Reference data size: Cells= 42 Genes= 8508
INFO [2020-07-06 13:20:35] plot_cnv_references:Number reference groups= 2
INFO [2020-07-06 13:20:35] plot_cnv_references:Plotting heatmap.
INFO [2020-07-06 13:20:35] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:20:35] Quantiles of plotted data range: 0.693386142642158,1.00394102388827,1.00394102388827,1.00394102388827,1.35009841572973
INFO [2020-07-06 13:20:35] plot_cnv_references:Writing reference data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.21_denoised.references.txt
INFO [2020-07-06 13:20:41]

Making the final infercnv heatmap

INFO [2020-07-06 13:20:42] ::plot_cnv:Start
INFO [2020-07-06 13:20:42] ::plot_cnv:Current data dimensions (r,c)=8508,184 Total=1569112.28502327 Min=0.530812412297805 Max=1.98172179650671.
INFO [2020-07-06 13:20:42] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2020-07-06 13:20:48] plot_cnv(): auto thresholding at: (0.649902 , 1.350098)
INFO [2020-07-06 13:20:48] plot_cnv_observation:Start
INFO [2020-07-06 13:20:48] Observation data size: Cells= 142 Genes= 8508
INFO [2020-07-06 13:20:48] clustering observations via method: ward.D
INFO [2020-07-06 13:20:48] plot_cnv_observation:Writing observation groupings/color.
INFO [2020-07-06 13:20:49] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:20:49] Quantiles of plotted data range: 0.649901584270269,1.00394102388827,1.00394102388827,1.00394102388827,1.35009841572973
INFO [2020-07-06 13:20:50] plot_cnv_references:Writing observation data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.observations.txt
INFO [2020-07-06 13:20:54] plot_cnv_references:Start
INFO [2020-07-06 13:20:54] Reference data size: Cells= 42 Genes= 8508
INFO [2020-07-06 13:20:54] plot_cnv_references:Number reference groups= 2
INFO [2020-07-06 13:20:54] plot_cnv_references:Plotting heatmap.
INFO [2020-07-06 13:20:54] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2020-07-06 13:20:54] Quantiles of plotted data range: 0.693386142642158,1.00394102388827,1.00394102388827,1.00394102388827,1.35009841572973
INFO [2020-07-06 13:20:54] plot_cnv_references:Writing reference data to C:\WINDOWS\Temp\RtmpMZweNO\file3d6850f13fab/infercnv.references.txt

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