HiCDCPlus differential interaction error
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Irene • 0
@99adfa00
Last seen 12 weeks ago
United States

Hello! I've been using HiC-DC+ to analyze some Micro-C data. I've been following along with the github documentation for calling differential loops using my own data, and everything has been going fine until I run hicdcdiff, where I get the below error. It seems to be something going wrong behind the scenes in the hicdcdiff function, so I'm not sure what to make of it. Any help is welcome!

 #Differential analysis using modified DESeq2 
 hicdcdiff(input_paths=list(WT=c(paste0(getwd(),'/WT-1-mapped-filt-mq30.txt.gz'), paste0(getwd(),'/WT-2-mapped-filt-mq30.txt.gz')),
                            KO=c(paste0(getwd(),'/KO-1-mapped-filt-mq30.txt.gz'), paste0(getwd(),'/KO-2-mapped-filt-mq30.txt.gz'))),
           filter_file=paste0(getwd(),'/hicdc_significant_indices.txt.gz'),
           output_path=paste0(getwd(),'/diff_analysis_example/'),
           fitType = 'mean',
           binsize=50000,
           diagnostics=TRUE)

Joining with `by = join_by(Dband, chr, startI, startJ)`
Joining with `by = join_by(Dband, chr, startI, startJ)`
Joining with `by = join_by(Dband, chr, startI, startJ)`
Joining with `by = join_by(Dband)`
converting counts to integer mode
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'start': unable to find an inherited method for function 'anchors' for signature '"NULL"'

And R session info is as follows:

sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.8 (Maipo)

Matrix products: default
BLAS/LAPACK: /lustre/fs4/risc_lab/scratch/risc_soft/miniconda3/envs/hicdc2/lib/libopenblasp-r0.3.24.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DESeq2_1.40.2                     SummarizedExperiment_1.30.2       Biobase_2.60.0                   
 [4] MatrixGenerics_1.12.2             matrixStats_1.1.0                 BSgenome.Hsapiens.UCSC.hg38_1.4.5
 [7] BSgenome_1.68.0                   rtracklayer_1.60.0                Biostrings_2.68.1                
[10] XVector_0.40.0                    GenomicRanges_1.50.2              GenomeInfoDb_1.36.1              
[13] IRanges_2.34.1                    S4Vectors_0.36.2                  BiocGenerics_0.46.0              
[16] data.table_1.14.8                 HiCDCPlus_1.8.0                  

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3         rstudioapi_0.15.0          magrittr_2.0.3             GenomicFeatures_1.50.4    
  [5] farver_2.1.1               rmarkdown_2.25             BiocIO_1.10.0              zlibbioc_1.46.0           
  [9] vctrs_0.6.4                memoise_2.0.1              Rsamtools_2.16.0           RCurl_1.98-1.13           
 [13] base64enc_0.1-3            htmltools_0.5.7            S4Arrays_1.0.4             progress_1.2.2            
 [17] curl_5.1.0                 Formula_1.2-5              htmlwidgets_1.6.2          Gviz_1.42.1               
 [21] cachem_1.0.8               GenomicAlignments_1.34.1   igraph_1.5.1               lifecycle_1.0.4           
 [25] pkgconfig_2.0.3            Matrix_1.6-3               R6_2.5.1                   fastmap_1.1.1             
 [29] GenomeInfoDbData_1.2.10    digest_0.6.33              colorspace_2.1-0           AnnotationDbi_1.60.2      
 [33] Hmisc_5.1-1                RSQLite_2.3.3              labeling_0.4.3             filelock_1.0.2            
 [37] fansi_1.0.5                httr_1.4.7                 compiler_4.3.2             bit64_4.0.5               
 [41] withr_2.5.2                htmlTable_2.4.2            backports_1.4.1            BiocParallel_1.32.6       
 [45] DBI_1.1.3                  R.utils_2.12.2             biomaRt_2.54.1             MASS_7.3-60               
 [49] rappdirs_0.3.3             DelayedArray_0.26.6        rjson_0.2.21               tools_4.3.2               
 [53] foreign_0.8-85             nnet_7.3-19                R.oo_1.25.0                glue_1.6.2                
 [57] restfulr_0.0.15            InteractionSet_1.26.1      grid_4.3.2                 checkmate_2.3.0           
 [61] cluster_2.1.4              generics_0.1.3             gtable_0.3.4               R.methodsS3_1.8.2         
 [65] tidyr_1.3.0                ensembldb_2.24.0           hms_1.1.3                  xml2_1.3.5                
 [69] utf8_1.2.4                 pillar_1.9.0               stringr_1.5.1              splines_4.3.2             
 [73] dplyr_1.1.3                BiocFileCache_2.6.1        lattice_0.22-5             deldir_1.0-9              
 [77] bit_4.0.5                  biovizBase_1.48.0          tidyselect_1.2.0           locfit_1.5-9.8            
 [81] knitr_1.45                 gridExtra_2.3              ProtGenerics_1.32.0        xfun_0.41                 
 [85] stringi_1.8.1              lazyeval_0.2.2             yaml_2.3.7                 evaluate_0.23             
 [89] codetools_0.2-19           interp_1.1-4               tibble_3.2.1               cli_3.6.1                 
 [93] rpart_4.1.21               munsell_0.5.0              GenomicInteractions_1.34.0 dichromat_2.0-0.1         
 [97] Rcpp_1.0.11                dbplyr_2.4.0               png_0.1-8                  XML_3.99-0.15             
[101] parallel_4.3.2             ggplot2_3.4.4              blob_1.2.4                 prettyunits_1.2.0         
[105] jpeg_0.1-10                latticeExtra_0.6-30        AnnotationFilter_1.24.0    bitops_1.0-7              
[109] VariantAnnotation_1.44.1   scales_1.2.1               purrr_1.0.2                crayon_1.5.2              
[113] rlang_1.1.2                KEGGREST_1.40.0
HiCDCPlus • 118 views
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