R Under development (unstable) (2026-04-26 r89963 ucrt) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(SCEGHiC) > > test_check("SCEGHiC") Generating aggregated data Aggregating cluster 0 Sample cells randomly. There are 11 samples Aggregating cluster 1 Sample cells randomly. There are 11 samples Generating aggregated data Aggregating cluster 0 There are 1 samples Generating aggregated data Aggregating cluster 0 Sample cells randomly. There are 11 samples Aggregating cluster 1 Sample cells randomly. There are 11 samples Processing chromosome chr2... Found 100 TSS loci on chr2. Calculating Hi-C weights for gene IL1R1... Calculating Hi-C weights for gene CHN1... Calculating Hi-C weights for gene RNF144A... Calculating Hi-C weights for gene EPB41L5... Calculating Hi-C weights for gene IQCA1... Calculating Hi-C weights for gene CCDC138... Calculating Hi-C weights for gene TOGARAM2... Calculating Hi-C weights for gene ACVR2A... Calculating Hi-C weights for gene SGPP2... Calculating Hi-C weights for gene WDR35... Calculating Hi-C weights for gene TMEM182... Calculating Hi-C weights for gene PDK1... Calculating Hi-C weights for gene UPP2... Calculating Hi-C weights for gene MYO3B... Calculating Hi-C weights for gene DTNB... Calculating Hi-C weights for gene TRABD2A... Calculating Hi-C weights for gene TTN... Calculating Hi-C weights for gene ACVR1C... Calculating Hi-C weights for gene ABCG8... Calculating Hi-C weights for gene SERPINE2... Calculating Hi-C weights for gene MGAT5... Calculating Hi-C weights for gene PLCD4... Calculating Hi-C weights for gene GTDC1... Calculating Hi-C weights for gene ANKAR... Calculating Hi-C weights for gene WDPCP... Calculating Hi-C weights for gene TANC1... Calculating Hi-C weights for gene GNLY... Calculating Hi-C weights for gene PGAP1... Calculating Hi-C weights for gene IKZF2... Calculating Hi-C weights for gene SH3RF3... Calculating Hi-C weights for gene LDAH... Calculating Hi-C weights for gene FAP... Calculating Hi-C weights for gene MFSD6... Calculating Hi-C weights for gene OSBPL6... Calculating Hi-C weights for gene RPS27A... Calculating Hi-C weights for gene CXCR4... Calculating Hi-C weights for gene ODC1... Calculating Hi-C weights for gene ZRANB3... Calculating Hi-C weights for gene EHBP1... Calculating Hi-C weights for gene MTA3... Calculating Hi-C weights for gene CTLA4... Calculating Hi-C weights for gene MAL... Calculating Hi-C weights for gene CD8A... Calculating Hi-C weights for gene KLHL29... Calculating Hi-C weights for gene ITM2C... Calculating Hi-C weights for gene AGAP1... Calculating Hi-C weights for gene CD8B... Calculating Hi-C weights for gene ZAP70... Calculating Hi-C weights for gene TACR1... Calculating Hi-C weights for gene LCLAT1... Calculating Hi-C weights for gene DUSP2... Calculating Hi-C weights for gene CD28... Calculating Hi-C weights for gene PARD3B... Calculating Hi-C weights for gene EFHD1... Calculating Hi-C weights for gene FBXO36... Calculating Hi-C weights for gene ARHGAP15... Calculating Hi-C weights for gene SCN2A... Calculating Hi-C weights for gene CAMKMT... Calculating Hi-C weights for gene ACYP2... Calculating Hi-C weights for gene CCDC141... Calculating Hi-C weights for gene KIF5C... Calculating Hi-C weights for gene APLF... Calculating Hi-C weights for gene LINC01250... Calculating Hi-C weights for gene LINC01376... Calculating Hi-C weights for gene MAP4K3-DT... Calculating Hi-C weights for gene LINC02580... Calculating Hi-C weights for gene LINC01119... Calculating Hi-C weights for gene EPHA4... Calculating Hi-C weights for gene LINC00342... Calculating Hi-C weights for gene CCNT2-AS1... Calculating Hi-C weights for gene LINC01876... Calculating Hi-C weights for gene MYO3B-AS1... Calculating Hi-C weights for gene FSIP2-AS1... Calculating Hi-C weights for gene LINC01473... Calculating Hi-C weights for gene FAM117B... Calculating Hi-C weights for gene NPAS2... Calculating Hi-C weights for gene ICOS... Calculating Hi-C weights for gene VWC2L... Calculating Hi-C weights for gene DIRC3... Calculating Hi-C weights for gene LINC01891... Calculating Hi-C weights for gene LINC01237... Calculating Hi-C weights for gene SNTG2... Calculating Hi-C weights for gene NCK2... Calculating Hi-C weights for gene PASK... Calculating Hi-C weights for gene NCKAP1... Calculating Hi-C weights for gene MGAT4A... Calculating Hi-C weights for gene PTPN4... Calculating Hi-C weights for gene DPP4... Calculating Hi-C weights for gene ID2... Calculating Hi-C weights for gene PLCL1... Calculating Hi-C weights for gene ARL4C... Calculating Hi-C weights for gene GALM... Calculating Hi-C weights for gene COL5A2... Calculating Hi-C weights for gene EDAR... Calculating Hi-C weights for gene SNED1... Calculating Hi-C weights for gene PLEKHH2... Calculating Hi-C weights for gene TMSB10... Calculating Hi-C weights for gene FSIP2... Calculating Hi-C weights for gene ADAM23... Calculating Hi-C weights for gene DNAH6... Finished calculating Hi-C weights for all genes. Processing chromosome chr3... Generating aggregated data Aggregating cluster 0 Sample cells randomly. There are 11 samples Aggregating cluster 1 Sample cells randomly. There are 11 samples Processing chromosome chr2... Found 100 TSS loci on chr2. Calculating Hi-C weights for gene IL1R1... Calculating Hi-C weights for gene CHN1... Calculating Hi-C weights for gene RNF144A... Calculating Hi-C weights for gene EPB41L5... Calculating Hi-C weights for gene IQCA1... Calculating Hi-C weights for gene CCDC138... Calculating Hi-C weights for gene TOGARAM2... Calculating Hi-C weights for gene ACVR2A... Calculating Hi-C weights for gene SGPP2... Calculating Hi-C weights for gene WDR35... Calculating Hi-C weights for gene TMEM182... Calculating Hi-C weights for gene PDK1... Calculating Hi-C weights for gene UPP2... Calculating Hi-C weights for gene MYO3B... Calculating Hi-C weights for gene DTNB... Calculating Hi-C weights for gene TRABD2A... Calculating Hi-C weights for gene TTN... Calculating Hi-C weights for gene ACVR1C... Calculating Hi-C weights for gene ABCG8... Calculating Hi-C weights for gene SERPINE2... Calculating Hi-C weights for gene MGAT5... Calculating Hi-C weights for gene PLCD4... Calculating Hi-C weights for gene GTDC1... Calculating Hi-C weights for gene ANKAR... Calculating Hi-C weights for gene WDPCP... Calculating Hi-C weights for gene TANC1... Calculating Hi-C weights for gene GNLY... Calculating Hi-C weights for gene PGAP1... Calculating Hi-C weights for gene IKZF2... Calculating Hi-C weights for gene SH3RF3... Calculating Hi-C weights for gene LDAH... Calculating Hi-C weights for gene FAP... Calculating Hi-C weights for gene MFSD6... Calculating Hi-C weights for gene OSBPL6... Calculating Hi-C weights for gene RPS27A... Calculating Hi-C weights for gene CXCR4... Calculating Hi-C weights for gene ODC1... Calculating Hi-C weights for gene ZRANB3... Calculating Hi-C weights for gene EHBP1... Calculating Hi-C weights for gene MTA3... Calculating Hi-C weights for gene CTLA4... Calculating Hi-C weights for gene MAL... Calculating Hi-C weights for gene CD8A... Calculating Hi-C weights for gene KLHL29... Calculating Hi-C weights for gene ITM2C... Calculating Hi-C weights for gene AGAP1... Calculating Hi-C weights for gene CD8B... Calculating Hi-C weights for gene ZAP70... Calculating Hi-C weights for gene TACR1... Calculating Hi-C weights for gene LCLAT1... Calculating Hi-C weights for gene DUSP2... Calculating Hi-C weights for gene CD28... Calculating Hi-C weights for gene PARD3B... Calculating Hi-C weights for gene EFHD1... Calculating Hi-C weights for gene FBXO36... Calculating Hi-C weights for gene ARHGAP15... Calculating Hi-C weights for gene SCN2A... Calculating Hi-C weights for gene CAMKMT... Calculating Hi-C weights for gene ACYP2... Calculating Hi-C weights for gene CCDC141... Calculating Hi-C weights for gene KIF5C... Calculating Hi-C weights for gene APLF... Calculating Hi-C weights for gene LINC01250... Calculating Hi-C weights for gene LINC01376... Calculating Hi-C weights for gene MAP4K3-DT... Calculating Hi-C weights for gene LINC02580... Calculating Hi-C weights for gene LINC01119... Calculating Hi-C weights for gene EPHA4... Calculating Hi-C weights for gene LINC00342... Calculating Hi-C weights for gene CCNT2-AS1... Calculating Hi-C weights for gene LINC01876... Calculating Hi-C weights for gene MYO3B-AS1... Calculating Hi-C weights for gene FSIP2-AS1... Calculating Hi-C weights for gene LINC01473... Calculating Hi-C weights for gene FAM117B... Calculating Hi-C weights for gene NPAS2... Calculating Hi-C weights for gene ICOS... Calculating Hi-C weights for gene VWC2L... Calculating Hi-C weights for gene DIRC3... Calculating Hi-C weights for gene LINC01891... Calculating Hi-C weights for gene LINC01237... Calculating Hi-C weights for gene SNTG2... Calculating Hi-C weights for gene NCK2... Calculating Hi-C weights for gene PASK... Calculating Hi-C weights for gene NCKAP1... Calculating Hi-C weights for gene MGAT4A... Calculating Hi-C weights for gene PTPN4... Calculating Hi-C weights for gene DPP4... Calculating Hi-C weights for gene ID2... Calculating Hi-C weights for gene PLCL1... Calculating Hi-C weights for gene ARL4C... Calculating Hi-C weights for gene GALM... Calculating Hi-C weights for gene COL5A2... Calculating Hi-C weights for gene EDAR... Calculating Hi-C weights for gene SNED1... Calculating Hi-C weights for gene PLEKHH2... Calculating Hi-C weights for gene TMSB10... Calculating Hi-C weights for gene FSIP2... Calculating Hi-C weights for gene ADAM23... Calculating Hi-C weights for gene DNAH6... Finished calculating Hi-C weights for all genes. Total predicted genes: 85 Running model for gene: IL1R1 Running model for gene: CHN1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.15" Running model for gene: RNF144A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.4" Running model for gene: EPB41L5 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: IQCA1 Running model for gene: CCDC138 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.41" Running model for gene: TOGARAM2 Running model for gene: ACVR2A Running model for gene: SGPP2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.13" Running model for gene: WDR35 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.2" Running model for gene: TMEM182 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.12" Running model for gene: PDK1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.45" Running model for gene: UPP2 Running model for gene: DTNB [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: TRABD2A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.43" Running model for gene: TTN [1] "The optimal penalty parameter (rho) selected by BIC is: 0.32" Running model for gene: ACVR1C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.28" Running model for gene: ABCG8 Running model for gene: SERPINE2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: MGAT5 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.38" Running model for gene: PLCD4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.21" Running model for gene: GTDC1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.43" Running model for gene: ANKAR [1] "The optimal penalty parameter (rho) selected by BIC is: 0.03" Running model for gene: GNLY [1] "The optimal penalty parameter (rho) selected by BIC is: 0.19" Running model for gene: PGAP1 Running model for gene: IKZF2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.07" Running model for gene: SH3RF3 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.3" Running model for gene: LDAH Running model for gene: FAP Running model for gene: MFSD6 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.22" Running model for gene: RPS27A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.16" Running model for gene: CXCR4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: ODC1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.28" Running model for gene: ZRANB3 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: MTA3 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.19" Running model for gene: CTLA4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.17" Running model for gene: CD8A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: KLHL29 Gene KLHL29 has too few Hi-C contact entries (<2). Skipping. Running model for gene: ITM2C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.45" Running model for gene: AGAP1 Gene AGAP1 has too few Hi-C contact entries (<2). Skipping. Running model for gene: CD8B [1] "The optimal penalty parameter (rho) selected by BIC is: 0.17" Running model for gene: ZAP70 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.31" Running model for gene: TACR1 Gene TACR1 has too few Hi-C contact entries (<2). Skipping. Running model for gene: LCLAT1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.41" Running model for gene: DUSP2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: CD28 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.42" Running model for gene: EFHD1 Running model for gene: FBXO36 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.35" Running model for gene: ARHGAP15 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: SCN2A Running model for gene: CAMKMT [1] "The optimal penalty parameter (rho) selected by BIC is: 0.22" Running model for gene: ACYP2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: CCDC141 [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: KIF5C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.27" Running model for gene: APLF [1] "The optimal penalty parameter (rho) selected by BIC is: 0.17" Running model for gene: LINC01250 Running model for gene: MAP4K3-DT [1] "The optimal penalty parameter (rho) selected by BIC is: 0.3" Running model for gene: LINC02580 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.34" Running model for gene: LINC01119 Running model for gene: EPHA4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.05" Running model for gene: CCNT2-AS1 Gene CCNT2-AS1 has too few Hi-C contact entries (<2). Skipping. Running model for gene: LINC01876 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: FAM117B [1] "The optimal penalty parameter (rho) selected by BIC is: 0.37" Running model for gene: NPAS2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: ICOS [1] "The optimal penalty parameter (rho) selected by BIC is: 0.34" Running model for gene: DIRC3 Running model for gene: LINC01891 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.15" Running model for gene: LINC01237 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.39" Running model for gene: SNTG2 Gene SNTG2 has too few Hi-C contact entries (<2). Skipping. Running model for gene: NCK2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.25" Running model for gene: PASK [1] "The optimal penalty parameter (rho) selected by BIC is: 0.3" Running model for gene: MGAT4A [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: PTPN4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.32" Running model for gene: DPP4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: ID2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.13" Running model for gene: PLCL1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.19" Running model for gene: ARL4C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.18" Running model for gene: GALM [1] "The optimal penalty parameter (rho) selected by BIC is: 0.11" Running model for gene: COL5A2 Running model for gene: EDAR [1] "The optimal penalty parameter (rho) selected by BIC is: 0.35" Running model for gene: SNED1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.07" Running model for gene: PLEKHH2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.05" Running model for gene: TMSB10 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.44" Running model for gene: ADAM23 [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: DNAH6 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.05" Generating aggregated data Aggregating cluster 0 Sample cells randomly. There are 11 samples Aggregating cluster 1 Sample cells randomly. There are 11 samples Processing chromosome chr2... Found 100 TSS loci on chr2. Calculating Hi-C weights for gene IL1R1... Calculating Hi-C weights for gene CHN1... Calculating Hi-C weights for gene RNF144A... Calculating Hi-C weights for gene EPB41L5... Calculating Hi-C weights for gene IQCA1... Calculating Hi-C weights for gene CCDC138... Calculating Hi-C weights for gene TOGARAM2... Calculating Hi-C weights for gene ACVR2A... Calculating Hi-C weights for gene SGPP2... Calculating Hi-C weights for gene WDR35... Calculating Hi-C weights for gene TMEM182... Calculating Hi-C weights for gene PDK1... Calculating Hi-C weights for gene UPP2... Calculating Hi-C weights for gene MYO3B... Calculating Hi-C weights for gene DTNB... Calculating Hi-C weights for gene TRABD2A... Calculating Hi-C weights for gene TTN... Calculating Hi-C weights for gene ACVR1C... Calculating Hi-C weights for gene ABCG8... Calculating Hi-C weights for gene SERPINE2... Calculating Hi-C weights for gene MGAT5... Calculating Hi-C weights for gene PLCD4... Calculating Hi-C weights for gene GTDC1... Calculating Hi-C weights for gene ANKAR... Calculating Hi-C weights for gene WDPCP... Calculating Hi-C weights for gene TANC1... Calculating Hi-C weights for gene GNLY... Calculating Hi-C weights for gene PGAP1... Calculating Hi-C weights for gene IKZF2... Calculating Hi-C weights for gene SH3RF3... Calculating Hi-C weights for gene LDAH... Calculating Hi-C weights for gene FAP... Calculating Hi-C weights for gene MFSD6... Calculating Hi-C weights for gene OSBPL6... Calculating Hi-C weights for gene RPS27A... Calculating Hi-C weights for gene CXCR4... Calculating Hi-C weights for gene ODC1... Calculating Hi-C weights for gene ZRANB3... Calculating Hi-C weights for gene EHBP1... Calculating Hi-C weights for gene MTA3... Calculating Hi-C weights for gene CTLA4... Calculating Hi-C weights for gene MAL... Calculating Hi-C weights for gene CD8A... Calculating Hi-C weights for gene KLHL29... Calculating Hi-C weights for gene ITM2C... Calculating Hi-C weights for gene AGAP1... Calculating Hi-C weights for gene CD8B... Calculating Hi-C weights for gene ZAP70... Calculating Hi-C weights for gene TACR1... Calculating Hi-C weights for gene LCLAT1... Calculating Hi-C weights for gene DUSP2... Calculating Hi-C weights for gene CD28... Calculating Hi-C weights for gene PARD3B... Calculating Hi-C weights for gene EFHD1... Calculating Hi-C weights for gene FBXO36... Calculating Hi-C weights for gene ARHGAP15... Calculating Hi-C weights for gene SCN2A... Calculating Hi-C weights for gene CAMKMT... Calculating Hi-C weights for gene ACYP2... Calculating Hi-C weights for gene CCDC141... Calculating Hi-C weights for gene KIF5C... Calculating Hi-C weights for gene APLF... Calculating Hi-C weights for gene LINC01250... Calculating Hi-C weights for gene LINC01376... Calculating Hi-C weights for gene MAP4K3-DT... Calculating Hi-C weights for gene LINC02580... Calculating Hi-C weights for gene LINC01119... Calculating Hi-C weights for gene EPHA4... Calculating Hi-C weights for gene LINC00342... Calculating Hi-C weights for gene CCNT2-AS1... Calculating Hi-C weights for gene LINC01876... Calculating Hi-C weights for gene MYO3B-AS1... Calculating Hi-C weights for gene FSIP2-AS1... Calculating Hi-C weights for gene LINC01473... Calculating Hi-C weights for gene FAM117B... Calculating Hi-C weights for gene NPAS2... Calculating Hi-C weights for gene ICOS... Calculating Hi-C weights for gene VWC2L... Calculating Hi-C weights for gene DIRC3... Calculating Hi-C weights for gene LINC01891... Calculating Hi-C weights for gene LINC01237... Calculating Hi-C weights for gene SNTG2... Calculating Hi-C weights for gene NCK2... Calculating Hi-C weights for gene PASK... Calculating Hi-C weights for gene NCKAP1... Calculating Hi-C weights for gene MGAT4A... Calculating Hi-C weights for gene PTPN4... Calculating Hi-C weights for gene DPP4... Calculating Hi-C weights for gene ID2... Calculating Hi-C weights for gene PLCL1... Calculating Hi-C weights for gene ARL4C... Calculating Hi-C weights for gene GALM... Calculating Hi-C weights for gene COL5A2... Calculating Hi-C weights for gene EDAR... Calculating Hi-C weights for gene SNED1... Calculating Hi-C weights for gene PLEKHH2... Calculating Hi-C weights for gene TMSB10... Calculating Hi-C weights for gene FSIP2... Calculating Hi-C weights for gene ADAM23... Calculating Hi-C weights for gene DNAH6... Finished calculating Hi-C weights for all genes. Total predicted genes: 85 Running model for gene: IL1R1 Running model for gene: CHN1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.15" Running model for gene: RNF144A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.4" Running model for gene: EPB41L5 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: IQCA1 Running model for gene: CCDC138 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.41" Running model for gene: TOGARAM2 Running model for gene: ACVR2A Running model for gene: SGPP2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.13" Running model for gene: WDR35 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.2" Running model for gene: TMEM182 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.12" Running model for gene: PDK1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.45" Running model for gene: UPP2 Running model for gene: DTNB [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: TRABD2A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.43" Running model for gene: TTN [1] "The optimal penalty parameter (rho) selected by BIC is: 0.32" Running model for gene: ACVR1C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.28" Running model for gene: ABCG8 Running model for gene: SERPINE2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: MGAT5 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.38" Running model for gene: PLCD4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.21" Running model for gene: GTDC1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.43" Running model for gene: ANKAR [1] "The optimal penalty parameter (rho) selected by BIC is: 0.03" Running model for gene: GNLY [1] "The optimal penalty parameter (rho) selected by BIC is: 0.19" Running model for gene: PGAP1 Running model for gene: IKZF2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.07" Running model for gene: SH3RF3 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.3" Running model for gene: LDAH Running model for gene: FAP Running model for gene: MFSD6 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.22" Running model for gene: RPS27A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.16" Running model for gene: CXCR4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: ODC1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.28" Running model for gene: ZRANB3 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: MTA3 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.19" Running model for gene: CTLA4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.17" Running model for gene: CD8A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: KLHL29 Gene KLHL29 has too few Hi-C contact entries (<2). Skipping. Running model for gene: ITM2C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.45" Running model for gene: AGAP1 Gene AGAP1 has too few Hi-C contact entries (<2). Skipping. Running model for gene: CD8B [1] "The optimal penalty parameter (rho) selected by BIC is: 0.17" Running model for gene: ZAP70 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.31" Running model for gene: TACR1 Gene TACR1 has too few Hi-C contact entries (<2). Skipping. Running model for gene: LCLAT1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.41" Running model for gene: DUSP2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: CD28 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.42" Running model for gene: EFHD1 Running model for gene: FBXO36 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.35" Running model for gene: ARHGAP15 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: SCN2A Running model for gene: CAMKMT [1] "The optimal penalty parameter (rho) selected by BIC is: 0.22" Running model for gene: ACYP2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: CCDC141 [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: KIF5C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.27" Running model for gene: APLF [1] "The optimal penalty parameter (rho) selected by BIC is: 0.17" Running model for gene: LINC01250 Running model for gene: MAP4K3-DT [1] "The optimal penalty parameter (rho) selected by BIC is: 0.3" Running model for gene: LINC02580 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.34" Running model for gene: LINC01119 Running model for gene: EPHA4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.05" Running model for gene: CCNT2-AS1 Gene CCNT2-AS1 has too few Hi-C contact entries (<2). Skipping. Running model for gene: LINC01876 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: FAM117B [1] "The optimal penalty parameter (rho) selected by BIC is: 0.37" Running model for gene: NPAS2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: ICOS [1] "The optimal penalty parameter (rho) selected by BIC is: 0.34" Running model for gene: DIRC3 Running model for gene: LINC01891 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.15" Running model for gene: LINC01237 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.39" Running model for gene: SNTG2 Gene SNTG2 has too few Hi-C contact entries (<2). Skipping. Running model for gene: NCK2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.25" Running model for gene: PASK [1] "The optimal penalty parameter (rho) selected by BIC is: 0.3" Running model for gene: MGAT4A [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: PTPN4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.32" Running model for gene: DPP4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: ID2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.13" Running model for gene: PLCL1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.19" Running model for gene: ARL4C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.18" Running model for gene: GALM [1] "The optimal penalty parameter (rho) selected by BIC is: 0.11" Running model for gene: COL5A2 Running model for gene: EDAR [1] "The optimal penalty parameter (rho) selected by BIC is: 0.35" Running model for gene: SNED1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.07" Running model for gene: PLEKHH2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.05" Running model for gene: TMSB10 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.44" Running model for gene: ADAM23 [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: DNAH6 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.05" [[1]] CustomTrack '' $Peaks AnnotationTrack 'Peaks' | genome: NA | active chromosome: chr2 | annotation features: 8 $Axis Genome axis 'Axis' $titles An object of class "ImageMap" Slot "coords": x1 y1 x2 y2 NA 6 6.0 18.15504 382.0 Peaks 6 382.0 18.15504 494.8 Axis 6 494.8 18.15504 570.0 Slot "tags": $title NA Peaks Axis "NA" "Peaks" "Axis" Generating aggregated data Aggregating cluster 0 Sample cells randomly. There are 11 samples Aggregating cluster 1 Sample cells randomly. There are 11 samples Processing chromosome chr2... Found 100 TSS loci on chr2. Calculating Hi-C weights for gene IL1R1... Calculating Hi-C weights for gene CHN1... Calculating Hi-C weights for gene RNF144A... Calculating Hi-C weights for gene EPB41L5... Calculating Hi-C weights for gene IQCA1... Calculating Hi-C weights for gene CCDC138... Calculating Hi-C weights for gene TOGARAM2... Calculating Hi-C weights for gene ACVR2A... Calculating Hi-C weights for gene SGPP2... Calculating Hi-C weights for gene WDR35... Calculating Hi-C weights for gene TMEM182... Calculating Hi-C weights for gene PDK1... Calculating Hi-C weights for gene UPP2... Calculating Hi-C weights for gene MYO3B... Calculating Hi-C weights for gene DTNB... Calculating Hi-C weights for gene TRABD2A... Calculating Hi-C weights for gene TTN... Calculating Hi-C weights for gene ACVR1C... Calculating Hi-C weights for gene ABCG8... Calculating Hi-C weights for gene SERPINE2... Calculating Hi-C weights for gene MGAT5... Calculating Hi-C weights for gene PLCD4... Calculating Hi-C weights for gene GTDC1... Calculating Hi-C weights for gene ANKAR... Calculating Hi-C weights for gene WDPCP... Calculating Hi-C weights for gene TANC1... Calculating Hi-C weights for gene GNLY... Calculating Hi-C weights for gene PGAP1... Calculating Hi-C weights for gene IKZF2... Calculating Hi-C weights for gene SH3RF3... Calculating Hi-C weights for gene LDAH... Calculating Hi-C weights for gene FAP... Calculating Hi-C weights for gene MFSD6... Calculating Hi-C weights for gene OSBPL6... Calculating Hi-C weights for gene RPS27A... Calculating Hi-C weights for gene CXCR4... Calculating Hi-C weights for gene ODC1... Calculating Hi-C weights for gene ZRANB3... Calculating Hi-C weights for gene EHBP1... Calculating Hi-C weights for gene MTA3... Calculating Hi-C weights for gene CTLA4... Calculating Hi-C weights for gene MAL... Calculating Hi-C weights for gene CD8A... Calculating Hi-C weights for gene KLHL29... Calculating Hi-C weights for gene ITM2C... Calculating Hi-C weights for gene AGAP1... Calculating Hi-C weights for gene CD8B... Calculating Hi-C weights for gene ZAP70... Calculating Hi-C weights for gene TACR1... Calculating Hi-C weights for gene LCLAT1... Calculating Hi-C weights for gene DUSP2... Calculating Hi-C weights for gene CD28... Calculating Hi-C weights for gene PARD3B... Calculating Hi-C weights for gene EFHD1... Calculating Hi-C weights for gene FBXO36... Calculating Hi-C weights for gene ARHGAP15... Calculating Hi-C weights for gene SCN2A... Calculating Hi-C weights for gene CAMKMT... Calculating Hi-C weights for gene ACYP2... Calculating Hi-C weights for gene CCDC141... Calculating Hi-C weights for gene KIF5C... Calculating Hi-C weights for gene APLF... Calculating Hi-C weights for gene LINC01250... Calculating Hi-C weights for gene LINC01376... Calculating Hi-C weights for gene MAP4K3-DT... Calculating Hi-C weights for gene LINC02580... Calculating Hi-C weights for gene LINC01119... Calculating Hi-C weights for gene EPHA4... Calculating Hi-C weights for gene LINC00342... Calculating Hi-C weights for gene CCNT2-AS1... Calculating Hi-C weights for gene LINC01876... Calculating Hi-C weights for gene MYO3B-AS1... Calculating Hi-C weights for gene FSIP2-AS1... Calculating Hi-C weights for gene LINC01473... Calculating Hi-C weights for gene FAM117B... Calculating Hi-C weights for gene NPAS2... Calculating Hi-C weights for gene ICOS... Calculating Hi-C weights for gene VWC2L... Calculating Hi-C weights for gene DIRC3... Calculating Hi-C weights for gene LINC01891... Calculating Hi-C weights for gene LINC01237... Calculating Hi-C weights for gene SNTG2... Calculating Hi-C weights for gene NCK2... Calculating Hi-C weights for gene PASK... Calculating Hi-C weights for gene NCKAP1... Calculating Hi-C weights for gene MGAT4A... Calculating Hi-C weights for gene PTPN4... Calculating Hi-C weights for gene DPP4... Calculating Hi-C weights for gene ID2... Calculating Hi-C weights for gene PLCL1... Calculating Hi-C weights for gene ARL4C... Calculating Hi-C weights for gene GALM... Calculating Hi-C weights for gene COL5A2... Calculating Hi-C weights for gene EDAR... Calculating Hi-C weights for gene SNED1... Calculating Hi-C weights for gene PLEKHH2... Calculating Hi-C weights for gene TMSB10... Calculating Hi-C weights for gene FSIP2... Calculating Hi-C weights for gene ADAM23... Calculating Hi-C weights for gene DNAH6... Finished calculating Hi-C weights for all genes. Total predicted genes: 85 Running model for gene: IL1R1 Running model for gene: CHN1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.15" Running model for gene: RNF144A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.4" Running model for gene: EPB41L5 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: IQCA1 Running model for gene: CCDC138 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.41" Running model for gene: TOGARAM2 Running model for gene: ACVR2A Running model for gene: SGPP2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.13" Running model for gene: WDR35 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.2" Running model for gene: TMEM182 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.12" Running model for gene: PDK1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.45" Running model for gene: UPP2 Running model for gene: DTNB [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: TRABD2A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.43" Running model for gene: TTN [1] "The optimal penalty parameter (rho) selected by BIC is: 0.32" Running model for gene: ACVR1C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.28" Running model for gene: ABCG8 Running model for gene: SERPINE2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: MGAT5 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.38" Running model for gene: PLCD4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.21" Running model for gene: GTDC1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.43" Running model for gene: ANKAR [1] "The optimal penalty parameter (rho) selected by BIC is: 0.03" Running model for gene: GNLY [1] "The optimal penalty parameter (rho) selected by BIC is: 0.19" Running model for gene: PGAP1 Running model for gene: IKZF2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.07" Running model for gene: SH3RF3 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.3" Running model for gene: LDAH Running model for gene: FAP Running model for gene: MFSD6 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.22" Running model for gene: RPS27A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.16" Running model for gene: CXCR4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: ODC1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.28" Running model for gene: ZRANB3 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: MTA3 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.19" Running model for gene: CTLA4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.17" Running model for gene: CD8A [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: KLHL29 Gene KLHL29 has too few Hi-C contact entries (<2). Skipping. Running model for gene: ITM2C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.45" Running model for gene: AGAP1 Gene AGAP1 has too few Hi-C contact entries (<2). Skipping. Running model for gene: CD8B [1] "The optimal penalty parameter (rho) selected by BIC is: 0.17" Running model for gene: ZAP70 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.31" Running model for gene: TACR1 Gene TACR1 has too few Hi-C contact entries (<2). Skipping. Running model for gene: LCLAT1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.41" Running model for gene: DUSP2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: CD28 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.42" Running model for gene: EFHD1 Running model for gene: FBXO36 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.35" Running model for gene: ARHGAP15 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.06" Running model for gene: SCN2A Running model for gene: CAMKMT [1] "The optimal penalty parameter (rho) selected by BIC is: 0.22" Running model for gene: ACYP2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: CCDC141 [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: KIF5C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.27" Running model for gene: APLF [1] "The optimal penalty parameter (rho) selected by BIC is: 0.17" Running model for gene: LINC01250 Running model for gene: MAP4K3-DT [1] "The optimal penalty parameter (rho) selected by BIC is: 0.3" Running model for gene: LINC02580 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.34" Running model for gene: LINC01119 Running model for gene: EPHA4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.05" Running model for gene: CCNT2-AS1 Gene CCNT2-AS1 has too few Hi-C contact entries (<2). Skipping. Running model for gene: LINC01876 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: FAM117B [1] "The optimal penalty parameter (rho) selected by BIC is: 0.37" Running model for gene: NPAS2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: ICOS [1] "The optimal penalty parameter (rho) selected by BIC is: 0.34" Running model for gene: DIRC3 Running model for gene: LINC01891 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.15" Running model for gene: LINC01237 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.39" Running model for gene: SNTG2 Gene SNTG2 has too few Hi-C contact entries (<2). Skipping. Running model for gene: NCK2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.25" Running model for gene: PASK [1] "The optimal penalty parameter (rho) selected by BIC is: 0.3" Running model for gene: MGAT4A [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: PTPN4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.32" Running model for gene: DPP4 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.14" Running model for gene: ID2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.13" Running model for gene: PLCL1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.19" Running model for gene: ARL4C [1] "The optimal penalty parameter (rho) selected by BIC is: 0.18" Running model for gene: GALM [1] "The optimal penalty parameter (rho) selected by BIC is: 0.11" Running model for gene: COL5A2 Running model for gene: EDAR [1] "The optimal penalty parameter (rho) selected by BIC is: 0.35" Running model for gene: SNED1 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.07" Running model for gene: PLEKHH2 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.05" Running model for gene: TMSB10 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.44" Running model for gene: ADAM23 [1] "The optimal penalty parameter (rho) selected by BIC is: 0" Running model for gene: DNAH6 [1] "The optimal penalty parameter (rho) selected by BIC is: 0.05" Computing hash Checking for 100 cell barcodes Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: Seqinfo [ FAIL 0 | WARN 3 | SKIP 3 | PASS 14 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'test-core.R:29:1', 'test-core.R:44:1', 'test-utils.R:41:1' [ FAIL 0 | WARN 3 | SKIP 3 | PASS 14 ] > > proc.time() user system elapsed 57.64 2.73 62.87