HiCDCPlus extract_hic_eigenvectors() only works with larger bin sizes (> =250kb )?
Entering edit mode
mlin18 • 0
Last seen 5 months ago
United States

I am using HiCDCPlus to find compartments A/B for HiC data, done with extract_hic_eigenvectors(). However, it seems that it only works for binsize>=250kb, which is the default value (even though the HiCDCPlus document says the default bin size is 100kb). Or is this caused by juicer?

This data set has the following bin sizes (in bp): 2500000 1000000 500000 250000 100000 50000 25000 10000 5000

for (sample in mySamples){
    hicfile=paste0(inDir, sample, "/", sample, "_inter_30.hic"),
    mode = "KR",
    binsize = 100000, # as well as 50000, 25000
    gen_ver = "hg38"

WARN [2023-03-28T14:44:20,611]  [Globals.java:138] [main]  Development mode is enabled
WARNING: Eigenvector calculation at high resolution can take a long time
Warning: File '/var/folders/gz/zzxt4sdj691ghc_vjzyqlk_00000gq/T//RtmpcTLMfx/filea0560f5435a.txt' has size 0. Returning a NULL data.table.Error in `dplyr::mutate()`:
ℹ In argument: `start = binsize * seq(0, nrow(out.df) - 1, 1)`.
Caused by error in `seq.default()`:
! wrong sign in 'by' argument
  1. HiCDCPlus::extract_hic_eigenvectors(...)
 13. base::seq.default(0, nrow(out.df) - 1, 1)
 14. base::stop("wrong sign in 'by' argument")
sessionInfo( )

R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.66.3                   rtracklayer_1.58.0               
 [4] Biostrings_2.66.0                 XVector_0.38.0                    GenomicRanges_1.50.2             
 [7] GenomeInfoDb_1.34.9               IRanges_2.32.0                    S4Vectors_0.36.2                 
[10] BiocGenerics_0.44.0               HiCDCPlus_1.6.0                  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.10                 lattice_0.20-45             Rsamtools_2.14.0           
 [4] digest_0.6.31               utf8_1.2.3                  BiocFileCache_2.6.1        
 [7] R6_2.5.1                    RSQLite_2.3.0               evaluate_0.20              
[10] httr_1.4.5                  pillar_1.9.0                zlibbioc_1.44.0            
[13] rlang_1.1.0                 curl_5.0.0                  rstudioapi_0.14            
[16] data.table_1.14.8           blob_1.2.4                  R.utils_2.12.2             
[19] R.oo_1.25.0                 Matrix_1.5-3                rmarkdown_2.21             
[22] splines_4.2.2               BiocParallel_1.32.6         RCurl_1.98-1.10            
[25] bit_4.0.5                   DelayedArray_0.24.0         compiler_4.2.2             
[28] xfun_0.38                   pkgconfig_2.0.3             htmltools_0.5.5            
[31] tidyselect_1.2.0            SummarizedExperiment_1.28.0 tibble_3.2.1               
[34] GenomeInfoDbData_1.2.9      codetools_0.2-19            matrixStats_0.63.0         
[37] XML_3.99-0.14               fansi_1.0.4                 withr_2.5.0                
[40] dbplyr_2.3.2                crayon_1.5.2                dplyr_1.1.1                
[43] GenomicAlignments_1.34.1    bitops_1.0-7                R.methodsS3_1.8.2          
[46] rappdirs_0.3.3              grid_4.2.2                  lifecycle_1.0.3            
[49] DBI_1.1.3                   magrittr_2.0.3              cachem_1.0.7               
[52] cli_3.6.1                   filelock_1.0.2              generics_0.1.3             
[55] vctrs_0.6.1                 rjson_0.2.21                restfulr_0.0.15            
[58] tools_4.2.2                 bit64_4.0.5                 Biobase_2.58.0             
[61] glue_1.6.2                  purrr_1.0.1                 MatrixGenerics_1.10.0      
[64] parallel_4.2.2              fastmap_1.1.1               yaml_2.3.7                 
[67] memoise_2.0.1               knitr_1.42                  BiocIO_1.8.0
HiCDCPlus • 212 views
Entering edit mode

Unfortunately, that seems to be your issue. There is a relevant thread here.


Login before adding your answer.

Traffic: 251 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6