inferCNV運(yùn)行記錄

> infercnv_obj = CreateInfercnvObject(delim="\t",
+                                     raw_counts_matrix=expFile,
+                                     annotations_file=groupFile,
+                                     gene_order_file= geneFile,
+                                     ref_group_names=c('Myeloid cell',"Lymphoid cell")) 
INFO [2021-12-09 08:30:32] Parsing matrix: expFile.txt
INFO [2021-12-09 08:31:03] Parsing gene order file: geneFile.txt
INFO [2021-12-09 08:31:03] Parsing cell annotations file: groupFile.txt
INFO [2021-12-09 08:31:03] ::order_reduce:Start.
INFO [2021-12-09 08:31:03] .order_reduce(): expr and order match.
INFO [2021-12-09 08:31:03] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 16360,7279 Total=164093919 Min=0 Max=2940.
INFO [2021-12-09 08:31:03] num genes removed taking into account provided gene ordering list: 1015 = 6.2041564792176% removed.
INFO [2021-12-09 08:31:03] -filtering out cells < 100 or > Inf, removing 0 % of cells
INFO [2021-12-09 08:31:06] validating infercnv_obj
> dir.create("CAG_inferCNV_Output_Cancercell_2")
> # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
> infercnv_obj = infercnv::run(infercnv_obj,
+                              cutoff=0.1, 
+                              out_dir="CAG_inferCNV_Output_Cancercell_2", 
+                              cluster_by_groups=TRUE, 
+                              denoise=TRUE,
+                              output_format = "pdf",
+                              HMM=F)
INFO [2021-12-09 08:31:36] ::process_data:Start
INFO [2021-12-09 08:31:36] Checking for saved results.
INFO [2021-12-09 08:31:36] 

    STEP 1: incoming data

INFO [2021-12-09 08:32:08] 

    STEP 02: Removing lowly expressed genes

INFO [2021-12-09 08:32:08] ::above_min_mean_expr_cutoff:Start
INFO [2021-12-09 08:32:08] Removing 7400 genes from matrix as below mean expr threshold: 0.1
INFO [2021-12-09 08:32:08] validating infercnv_obj
INFO [2021-12-09 08:32:08] There are 7945 genes and 7279 cells remaining in the expr matrix.
INFO [2021-12-09 08:32:11] no genes removed due to min cells/gene filter
INFO [2021-12-09 08:32:36] 

    STEP 03: normalization by sequencing depth

INFO [2021-12-09 08:32:36] normalizing counts matrix by depth
INFO [2021-12-09 08:32:37] Computed total sum normalization factor as median libsize: 21485.000000
INFO [2021-12-09 08:33:03] 

    STEP 04: log transformation of data

INFO [2021-12-09 08:33:03] transforming log2xplus1()
INFO [2021-12-09 08:33:29] 

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

INFO [2021-12-09 08:33:29] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-12-09 08:33:29] subtracting mean(normal) per gene per cell across all data
INFO [2021-12-09 08:33:34] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-12-09 08:34:16] 

    STEP 09: apply max centered expression threshold: 3

INFO [2021-12-09 08:34:16] ::process_data:setting max centered expr, threshold set to: +/-:  3
INFO [2021-12-09 08:34:54] 

    STEP 10: Smoothing data per cell by chromosome

INFO [2021-12-09 08:34:54] smooth_by_chromosome: chr: chr1
INFO [2021-12-09 08:35:00] smooth_by_chromosome: chr: chr2
INFO [2021-12-09 08:35:08] smooth_by_chromosome: chr: chr3
INFO [2021-12-09 08:35:14] smooth_by_chromosome: chr: chr4
INFO [2021-12-09 08:35:21] smooth_by_chromosome: chr: chr5
INFO [2021-12-09 08:35:29] smooth_by_chromosome: chr: chr6
INFO [2021-12-09 08:35:36] smooth_by_chromosome: chr: chr7
INFO [2021-12-09 08:35:43] smooth_by_chromosome: chr: chr8
INFO [2021-12-09 08:35:50] smooth_by_chromosome: chr: chr9
INFO [2021-12-09 08:35:58] smooth_by_chromosome: chr: chr10
INFO [2021-12-09 08:36:04] smooth_by_chromosome: chr: chr11
INFO [2021-12-09 08:36:12] smooth_by_chromosome: chr: chr12
INFO [2021-12-09 08:36:19] smooth_by_chromosome: chr: chr13
INFO [2021-12-09 08:36:25] smooth_by_chromosome: chr: chr14
INFO [2021-12-09 08:36:32] smooth_by_chromosome: chr: chr15
INFO [2021-12-09 08:36:38] smooth_by_chromosome: chr: chr16
INFO [2021-12-09 08:36:45] smooth_by_chromosome: chr: chr17
INFO [2021-12-09 08:36:52] smooth_by_chromosome: chr: chr18
INFO [2021-12-09 08:36:58] smooth_by_chromosome: chr: chr19
INFO [2021-12-09 08:37:44] 

    STEP 11: re-centering data across chromosome after smoothing

INFO [2021-12-09 08:37:44] ::center_smooth across chromosomes per cell
INFO [2021-12-09 08:38:34] 

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

INFO [2021-12-09 08:38:34] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2021-12-09 08:38:34] subtracting mean(normal) per gene per cell across all data
INFO [2021-12-09 08:38:38] -subtracting expr per gene, use_bounds=TRUE
INFO [2021-12-09 08:39:19] 

    STEP 14: invert log2(FC) to FC

INFO [2021-12-09 08:39:19] invert_log2(), computing 2^x
INFO [2021-12-09 08:40:04] 

    STEP 15: Clustering samples (not defining tumor subclusters)

INFO [2021-12-09 08:40:04] define_signif_tumor_subclusters(p_val=0.1
INFO [2021-12-09 08:40:04] define_signif_tumor_subclusters(), tumor: C01
INFO [2021-12-09 08:43:56] cut tree into: 1 groups
INFO [2021-12-09 08:43:56] -processing C01,C01_s1
INFO [2021-12-09 08:43:56] define_signif_tumor_subclusters(), tumor: C02
INFO [2021-12-09 08:45:09] cut tree into: 1 groups
INFO [2021-12-09 08:45:09] -processing C02,C02_s1
INFO [2021-12-09 08:45:09] define_signif_tumor_subclusters(), tumor: C03
INFO [2021-12-09 08:45:45] cut tree into: 1 groups
INFO [2021-12-09 08:45:45] -processing C03,C03_s1
INFO [2021-12-09 08:45:45] define_signif_tumor_subclusters(), tumor: C04
INFO [2021-12-09 08:45:59] cut tree into: 1 groups
INFO [2021-12-09 08:45:59] -processing C04,C04_s1
INFO [2021-12-09 08:45:59] define_signif_tumor_subclusters(), tumor: C05
INFO [2021-12-09 08:46:07] cut tree into: 1 groups
INFO [2021-12-09 08:46:07] -processing C05,C05_s1
INFO [2021-12-09 08:46:07] define_signif_tumor_subclusters(), tumor: C06
INFO [2021-12-09 08:46:13] cut tree into: 1 groups
INFO [2021-12-09 08:46:13] -processing C06,C06_s1
INFO [2021-12-09 08:46:13] define_signif_tumor_subclusters(), tumor: C07
INFO [2021-12-09 08:46:16] cut tree into: 1 groups
INFO [2021-12-09 08:46:16] -processing C07,C07_s1
INFO [2021-12-09 08:46:16] define_signif_tumor_subclusters(), tumor: C08
INFO [2021-12-09 08:46:18] cut tree into: 1 groups
INFO [2021-12-09 08:46:18] -processing C08,C08_s1
INFO [2021-12-09 08:46:18] define_signif_tumor_subclusters(), tumor: Myeloid cell
INFO [2021-12-09 08:46:34] cut tree into: 1 groups
INFO [2021-12-09 08:46:34] -processing Myeloid cell,Myeloid cell_s1
INFO [2021-12-09 08:46:34] define_signif_tumor_subclusters(), tumor: Lymphoid cell
INFO [2021-12-09 08:46:35] cut tree into: 1 groups
INFO [2021-12-09 08:46:35] -processing Lymphoid cell,Lymphoid cell_s1
INFO [2021-12-09 08:48:00] ::plot_cnv:Start
INFO [2021-12-09 08:48:00] ::plot_cnv:Current data dimensions (r,c)=7945,7279 Total=58098065.8675027 Min=0.466829497259287 Max=1.83737474632447.
INFO [2021-12-09 08:48:01] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-12-09 08:49:02] plot_cnv(): auto thresholding at: (0.789432 , 1.219781)
INFO [2021-12-09 08:49:04] plot_cnv_observation:Start
INFO [2021-12-09 08:49:04] Observation data size: Cells= 6384 Genes= 7945
INFO [2021-12-09 08:49:05] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-12-09 08:49:05] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-12-09 08:49:05] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-12-09 08:49:05] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-12-09 08:49:18] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-12-09 08:49:18] Quantiles of plotted data range: 0.789432426227872,0.957956912793076,1,1.04388193683948,1.21978089708106
INFO [2021-12-09 08:49:24] plot_cnv_observations:Writing observation data to CAG_inferCNV_Output_Cancercell_2/infercnv.preliminary.observations.txt
INFO [2021-12-09 08:50:18] plot_cnv_references:Start
INFO [2021-12-09 08:50:18] Reference data size: Cells= 895 Genes= 7945
INFO [2021-12-09 08:50:35] plot_cnv_references:Number reference groups= 2
INFO [2021-12-09 08:50:35] plot_cnv_references:Plotting heatmap.
INFO [2021-12-09 08:50:36] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-12-09 08:50:36] Quantiles of plotted data range: 0.789432426227872,0.96688495685827,1,1.03158820364972,1.21978089708106
INFO [2021-12-09 08:50:37] plot_cnv_references:Writing reference data to CAG_inferCNV_Output_Cancercell_2/infercnv.preliminary.references.txt
INFO [2021-12-09 08:50:47] 

    STEP 21: Denoising

INFO [2021-12-09 08:50:47] ::process_data:Remove noise, noise threshold defined via ref mean sd_amplifier:  1.5
INFO [2021-12-09 08:50:47] denoising using mean(normal) +- sd_amplifier * sd(normal) per gene per cell across all data
INFO [2021-12-09 08:50:47] :: **** clear_noise_via_ref_quantiles **** : removing noise between bounds:  0.917293991432762 - 1.08631551518791
INFO [2021-12-09 08:51:10] ::plot_cnv:Start
INFO [2021-12-09 08:51:10] ::plot_cnv:Current data dimensions (r,c)=7945,7279 Total=58285113.1960789 Min=0.466829497259287 Max=1.83737474632447.
INFO [2021-12-09 08:51:10] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-12-09 08:52:10] plot_cnv(): auto thresholding at: (0.795901 , 1.219781)
INFO [2021-12-09 08:52:12] plot_cnv_observation:Start
INFO [2021-12-09 08:52:12] Observation data size: Cells= 6384 Genes= 7945
INFO [2021-12-09 08:52:13] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-12-09 08:52:13] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-12-09 08:52:13] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-12-09 08:52:13] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-12-09 08:52:24] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-12-09 08:52:24] Quantiles of plotted data range: 0.795901109464115,1.00180475331034,1.00180475331034,1.00180475331034,1.21978089708106
INFO [2021-12-09 08:52:31] plot_cnv_observations:Writing observation data to CAG_inferCNV_Output_Cancercell_2/infercnv.21_denoised.observations.txt
INFO [2021-12-09 08:53:23] plot_cnv_references:Start
INFO [2021-12-09 08:53:23] Reference data size: Cells= 895 Genes= 7945
INFO [2021-12-09 08:53:40] plot_cnv_references:Number reference groups= 2
INFO [2021-12-09 08:53:40] plot_cnv_references:Plotting heatmap.
INFO [2021-12-09 08:53:41] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-12-09 08:53:41] Quantiles of plotted data range: 0.795901109464115,1.00180475331034,1.00180475331034,1.00180475331034,1.21978089708106
INFO [2021-12-09 08:53:42] plot_cnv_references:Writing reference data to CAG_inferCNV_Output_Cancercell_2/infercnv.21_denoised.references.txt
INFO [2021-12-09 08:54:11] 

## Making the final infercnv heatmap ##
INFO [2021-12-09 08:54:12] ::plot_cnv:Start
INFO [2021-12-09 08:54:12] ::plot_cnv:Current data dimensions (r,c)=7945,7279 Total=58285113.1960789 Min=0.466829497259287 Max=1.83737474632447.
INFO [2021-12-09 08:54:12] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2021-12-09 08:55:11] plot_cnv(): auto thresholding at: (0.780219 , 1.219781)
INFO [2021-12-09 08:55:13] plot_cnv_observation:Start
INFO [2021-12-09 08:55:13] Observation data size: Cells= 6384 Genes= 7945
INFO [2021-12-09 08:55:14] plot_cnv_observation:Writing observation groupings/color.
INFO [2021-12-09 08:55:14] plot_cnv_observation:Done writing observation groupings/color.
INFO [2021-12-09 08:55:14] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2021-12-09 08:55:14] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2021-12-09 08:55:26] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-12-09 08:55:26] Quantiles of plotted data range: 0.780219102918943,1.00180475331034,1.00180475331034,1.00180475331034,1.21978089708106
INFO [2021-12-09 08:55:32] plot_cnv_observations:Writing observation data to CAG_inferCNV_Output_Cancercell_2/infercnv.observations.txt
INFO [2021-12-09 08:56:24] plot_cnv_references:Start
INFO [2021-12-09 08:56:24] Reference data size: Cells= 895 Genes= 7945
INFO [2021-12-09 08:56:41] plot_cnv_references:Number reference groups= 2
INFO [2021-12-09 08:56:41] plot_cnv_references:Plotting heatmap.
INFO [2021-12-09 08:56:42] Colors for breaks:  #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2021-12-09 08:56:42] Quantiles of plotted data range: 0.780219102918943,1.00180475331034,1.00180475331034,1.00180475331034,1.21978089708106
INFO [2021-12-09 08:56:43] plot_cnv_references:Writing reference data to CAG_inferCNV_Output_Cancercell_2/infercnv.references.txt

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