Error in library(TCGA2STAT) : there is no package called ‘TCGA2STAT’ In addition: Warning message: replacing previous import ‘AUCell::cbind’ by ‘SingleCellExperiment::cbind’ when loading ‘SCENIC’ [1] "GISTHs2" Warning: The 'show_progress' argument is deprecated as of v0.3. Use 'verbosity' instead. (in sctransform::vst) Calculating cell attributes from input UMI matrix: log_umi Variance stabilizing transformation of count matrix of size 15509 by 2493 Model formula is y ~ log_umi Get Negative Binomial regression parameters per gene Using 2000 genes, 2493 cells | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Found 73 outliers - those will be ignored in fitting/regularization step Second step: Get residuals using fitted parameters for 15509 genes | | | 0% | |== | 3% | |==== | 6% | |======= | 9% | |========= | 12% | |=========== | 16% | |============= | 19% | |=============== | 22% | |================== | 25% | |==================== | 28% | |====================== | 31% | |======================== | 34% | |========================== | 38% | |============================ | 41% | |=============================== 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|==================================================================== | 97% | |======================================================================| 100% Computing corrected count matrix for 15509 genes | | | 0% | |== | 3% | |==== | 6% | |======= | 9% | |========= | 12% | |=========== | 16% | |============= | 19% | |=============== | 22% | |================== | 25% | |==================== | 28% | |====================== | 31% | |======================== | 34% | |========================== | 38% | |============================ | 41% | |=============================== | 44% | |================================= | 47% | |=================================== | 50% | |===================================== | 53% | |======================================= | 56% | |========================================== | 59% | |============================================ | 62% | |============================================== | 66% | |================================================ | 69% | 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PC_ 1 Positive: IGFBP7, TAGLN, TMSB10, ADIRF, IGFBP3, MYL9, ACTA2, MFGE8, MCAM, DEPP1 FN1, CD74, CRIP1, S100A4, BGN, MYH11, PPP1R14A, TM4SF1, DUSP1, A2M MT2A, RHOB, S100A6, HLA-DRA, GJA4, CLDN5, NDUFA4L2, KLF2, HES4, FRZB Negative: CTSL, PLAT, CA2, DLK1, TIMP1, MFAP4, SFRP1, IGFBP5, FHL2, DPT TGFBI, PROM1, CTSC, HSPB6, CD81, PDGFRA, ATP1B1, LY6H, SPON2, KCNK3 B2M, LGALS3BP, TIMP3, BARX1, TMEM176B, CPE, AC008397.2, TSC22D1, C11orf96, CLU PC_ 2 Positive: CD74, HLA-DRA, FTL, HLA-DPA1, FTH1, HLA-DPB1, HLA-DRB1, TMSB10, TPT1, HLA-DQB1 LYZ, HLA-DQA1, CD52, C1QA, TMSB4X, CST3, C1QB, HLA-DRB5, B2M, TYROBP C1QC, DNASE1L3, AIF1, LGALS2, LCP1, AC020656.1, FCER1G, UBA52, EEF1A1, IFITM1 Negative: IGFBP7, ADIRF, PLAT, TAGLN, ACTA2, FN1, MYL9, IGFBP3, MCAM, CTSL DEPP1, A2M, SFRP1, RHOB, IGFBP5, MFGE8, MYH11, MGP, TM4SF1, FBLN5 NDUFA4L2, PPP1R14A, VIM, GJA4, FRZB, TINAGL1, PLAC9, AEBP1, BGN, HES4 PC_ 3 Positive: TPT1, TMSB4X, FTL, EEF1A1, IGF2.1, ATP5F1E, FTH1, UQCRB, TOMM7, NACA YBX1, LGALS1, COX7C, HSPB6, UQCR11, UBA52, ATP5MD, COX7A1, OST4, RGS5 S100A13, RACK1, GAPDH, ATP5MG, SELENOW, GUK1, NDUFA4, NPM1, SERF2, TMA7 Negative: CD74, CST3, IGFBP5, HLA-DRA, HLA-B, HLA-DRB1, LYZ, ACTB, AC092069.1, LY6E CEBPD, AC020656.1, ITM2B, HLA-C, C7, MFAP4, HLA-A, HLA-DRB5, STAT2, HLA-DQB1 CALR, COL6A1, HLA-DPA1, SERPING1, EMILIN1, CTSL, HLA-E, HLA-DQA1, TAPBP, IFI27 PC_ 4 Positive: B2M, IFITM3, IFITM1, HLA-B, CA2, HLA-C, CST3, MFAP4, CEBPD, LY6E FTH1, BST2, IFI27, FTL, ISG15, C11orf96, LAP3, DPT, TIMP1, CTSL CXCL10, LMO2, FHL2, HSPA8, SKP1, ITM2B, ACTG1, IL18BP, PTP4A3, MT2A Negative: AC092069.1, LRRC75A, TMSB4X, ACTB, MALAT1, SFRP1, CTNNB1, LYZ, AC020656.1, PHKG1 IGFBP5, PLAT, C1orf56, CCND2, CCDC152, AC009133.1, IGF2.1, CALR, SLC12A2, EIF5A PPP1CB, AD000090.1, SUMF2, NORAD, ARPC4, AL450306.1, TPT1, IGKC, AC005944.1, SPTBN1 PC_ 5 Positive: HLA-DRA, CA2, AC020656.1, HLA-DPA1, LYZ, AC092069.1, CD74, ATP1B1, FHL2, VIM SKP1, SLC12A2, B2M, SRP14, TSC22D1, MGP, FGL2, HLA-DQA1, PROM1, HLA-DPB1 TMSB4X, CTNNB1, LRRC75A, HLA-DRB1, ACTB, PPIA, COX7C, DSTN, ACTA2, C1orf56 Negative: DLK1, IGKC, ISG15, IFI27, MALAT1, LY6E, COL6A2, EMILIN1, CD52, SERF2 HLA-A, LY6H, IL32, CCL5, IGFBP4, MXRA8, IFI6, C3, IL7R, LGALS1 ELOB, IFITM1, GUK1, C9orf16, S100A4, AD000090.1, FTL, SELENOM, KLRB1, TRBC2 Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation' This message will be shown once per session 11:15:28 UMAP embedding parameters a = 0.9922 b = 1.112 11:15:28 Read 2493 rows and found 10 numeric columns 11:15:28 Using Annoy for neighbor search, n_neighbors = 30 11:15:28 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 11:15:29 Writing NN index file to temp file /tmp/RtmpJfmFSe/file44111a1e9270 11:15:29 Searching Annoy index using 1 thread, search_k = 3000 11:15:30 Annoy recall = 100% 11:15:31 Commencing smooth kNN distance calibration using 1 thread 11:15:32 Initializing from normalized Laplacian + noise 11:15:32 Commencing optimization for 500 epochs, with 95442 positive edges 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 11:15:44 Optimization finished null device 1 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 2493 Number of edges: 81493 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.6692 Number of communities: 8 Elapsed time: 0 seconds [1] 3000 2493 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 3 5 6 7 7 5 11 9 8 13 14 14 16 15 17 19 19 20 21 23 24 [1] "11" $m_HACE1 [1] "HACE1" "TWNK" "ATG4A" "MOB3C" "SIN3B" "TRNAU1AP" "PRKAB2" $m_SRGAP3 [1] "SRGAP3" "GPC6" "FAM222A" "DENND2A" "ANO5" "KIF1BP" "GABPB1" $m_CA2 [1] "CA2" "THAP8" "PLAUR" "ETFBKMT" "ARFGAP1" "ERLIN1" [7] "RBMS2" "ZFP82" "TIMP1" "ZNF263" "BLOC1S2" "GTF2IRD2B" [13] "RAB34" "C3orf70" "PLCD4" "GOT1" "PCYT1B" "RIC8A" [19] "FHL2" "TRPC3" "DCTPP1" "MSRB1" "HOMER3" "DDIT4" [25] "TMEM201" "POLI" "GABARAPL2" "MLX" "GOT2" "PPWD1" [31] "HSBP1" "MELTF-AS1" "ZNF747" "CTSL" "TMEM140" "FAM8A1" [37] "BCAR1" "MUM1" "POLK" "CFAP70" "MAN1B1" "MFAP4" $m_MALAT1 [1] "MALAT1" "DLK1" "IGFBP4" "COL6A2" "EMILIN1" "MXRA8" "FBLN1" [8] "PLAT" "PODN" "C9orf16" "LTBP4" "CCSAP" "LAMB2" $m_TPT1 [1] "TPT1" "TMSB4X" "IGF2.1" "FTL" "EEF1A1" "ATP5F1E" "YBX1" $m_FAAP100 [1] "FAAP100" "FILIP1" "VPS52" "FAM49A" "PCED1B" [6] "MRM1" "DDR1" "CCDC58" "KIF26B" "CLEC11A" [11] "AC009228.1" "NCS1" "MLKL" "STX3" "SERTAD1" [16] "HSD11B1" "TNRC6A" "AC012615.1" "LINC02482" "MPO" [21] "MAP3K8" "SSRP1" "SYCP2" "AC017100.1" "TPST2" [26] "CTSC" "ZNF181" "ZNF688" "HSD17B11" "AC044839.1" [31] "PSMB7" "AC100803.3" $m_HAPLN2 [1] "HAPLN2" "PTN" "AASS" "NUP50" "WWC2" [6] "UST" "AC098850.3" "PYM1" "ALDH1L2" "ZNF736" [11] "NGDN" "VSIG10" "ATG2A" "FANCI" "BCL9" $m_CD74 [1] "CD74" "HLA-DRA" "HLA-DRB1" "HLA-DPA1" "HLA-DPB1" "TMSB10" [7] "CD52" "HLA-DQA1" "LYZ" "CST3" "IFITM1" "HLA-DQB1" [13] "HLA-DRB5" "CXCL10" "LGALS2" "LTB" "FTH1" "B2M" [19] "C1QA" "LY6E" "C1QB" "ISG15" "TYROBP" "FCER1G" [25] "TRBC2" "HLA-B" "LIMD2" "DNASE1L3" "RGS10" "IL32" [31] "C1QC" "LAPTM5" "ITGB2" "IFITM3" "LCP1" "CCL4L2" [37] "CCL5" "IFI27" "CCL4" "TRBC1" "CORO1A" "COTL1" [43] "MPEG1" "LSP1" "NKG7" "SRGN" "LGALS9" $m_AC092069.1 [1] "AC092069.1" "LRRC75A" "C1orf56" "PHKG1" "ACTB" [6] "CTNNB1" "AC009133.1" "CCDC152" "SUMF2" "AL450306.1" [11] "AC020656.1" "TRA2A" "SLC12A2" "IGFBP5" "SLITRK2" [16] "HNRNPH1" "CALR" "AC005944.1" "MFSD8" "IFI6" [21] "ATP1B1" "EIF5A" "AC010761.1" "NUDT4" "SOX4" [26] "CCND2" "NORAD" "CLEC7A" "ARPC4" "PPP1CB" [31] "AC005921.2" "PDGFC" "FBXW7" "C7" "PPOX" [36] "TAOK2" "CDC42" "PRKAG2-AS1" "CENPM" "CTBP1" [41] "WSB1" "ATP1B2" "FGD1" "ADAM17" "TMEM150C" [46] "RPH3AL" "RETREG3" "SPTBN1" "RFFL" "ZNF557" [51] "BRCA1" "SMU1" "ZNF267" "SLC29A4" "STAT2" [56] "SOCS7" "YAP1" "NR2F1" "FLYWCH2" "RBM24" [61] "COQ10B" "VMO1" "BAIAP2L1" "TTN-AS1" "LENG8" [66] "PRKAG2" "LACTB2" "GOPC" "CTSH" "RILPL2" [71] "RAB12" $m_IGKC [1] "IGKC" "IGHG3" "SLC2A6" "GOLGA8A" "BRINP3" "SEC31B" [7] "IGHG1" "TVP23A" "SIGLEC10" "PNP" "ADGRD1" "BCL7A" [13] "OSBPL3" "IL12RB1" "CXCL9" "PPP1R13B" "IGHGP" "SKI" [19] "TAF5" "HMOX1" "JCHAIN" "RCOR3" "CCDC92" "NTHL1" [25] "FBXL19" "GNA11" "VPS72" "TAZ" "RWDD2B" "SCT" [31] "ADAM15" "RRBP1" "LRRTM1" "PSPC1" "APH1B" "ITGA6" $m_IGFBP7 [1] "IGFBP7" "ADIRF" "TAGLN" "MYL9" "ACTA2" "DEPP1" [7] "A2M" "EPAS1" "FABP5" "IGFBP3" "DUSP1" "RHOB" [13] "PLVAP" "MT2A" "MFGE8" "KLF2" "S100A6" "NDUFA4L2" [19] "S100A4" "CRIP1" "RAMP2" "TINAGL1" "HSPG2" "GJA4" [25] "AQP1" "ACKR1" Warning message: Using `as.character()` on a quosure is deprecated as of rlang 0.3.0. Please use `as_label()` or `as_name()` instead. This warning is displayed once per session. null device 1 Calculating cluster 0 Calculating cluster 1 Calculating cluster 2 Calculating cluster 3 Calculating cluster 4 Calculating cluster 5 Calculating cluster 6 Calculating cluster 7 Warning message: CombinePlots is being deprecated. Plots should now be combined using the patchwork system. Calculating cluster m_HACE1 Calculating cluster m_SRGAP3 Calculating cluster m_CA2 Calculating cluster m_MALAT1 Calculating cluster m_TPT1 Calculating cluster m_FAAP100 Calculating cluster m_HAPLN2 Calculating cluster m_CD74 Calculating cluster m_AC092069.1 Calculating cluster m_IGKC Calculating cluster m_IGFBP7 Warning message: CombinePlots is being deprecated. Plots should now be combined using the patchwork system. null device 1