v4C - rowSum ERROR
matteozoia4 opened this issue · comments
Dear all,
I am trying to extract the v4C from a .cool file.
It works with another view point, but with this one "chr8:57483000-57493000", it gives an error, why?
v4C_Sap30_Prom_10kb <- virtual4C(hic, viewpoint = GRanges("chr8:57483000-57493000"))
Error in rowSums(cm[, regions_in_viewpoint], na.rm = TRUE) :
'x' must be an array of at least two dimensions
How can I fix this?
Best regards and many thanks!
Link to the .cool file : https://we.tl/t-oi2vbQR8SW
I believe this error might be due to the fact that your query GRanges is rather narrow. If this is the issue, this bug could be fixed by a recent update in the package (9c76595). You can update HiContacts to the development version from GitHub using the following command:
remotes::install_github(js2264/HiContacts)
I do not have access to a computer right now, but I will check this as soon as I have a machine at my disposal.
Many thanks for the prompt response!
The error persists unfortunately.
I am able to compute a v4C profile from the file and command you provided me:
> hic <- import('GSE161259_ES_chr8_55400000_59200000_MAPQ30.40kb.cool')
> v4C <- virtual4C(hic, viewpoint = GenomicRanges::GRanges("chr8:57483000-57493000"))
Warning message:
In asMethod(object) :
sparse->dense coercion: allocating vector of size 34.8 GiB
> v4C
GRanges object with 68301 ranges and 4 metadata columns:
seqnames ranges strand | score viewpoint center in_viewpoint
<Rle> <IRanges> <Rle> | <numeric> <character> <numeric> <logical>
[1] chr1 1-40000 * | 0 chr8:57483000-57493000 20000.5 FALSE
[2] chr1 40001-80000 * | 0 chr8:57483000-57493000 60000.5 FALSE
[3] chr1 80001-120000 * | 0 chr8:57483000-57493000 100000.5 FALSE
[4] chr1 120001-160000 * | 0 chr8:57483000-57493000 140000.5 FALSE
[5] chr1 160001-200000 * | 0 chr8:57483000-57493000 180000.5 FALSE
... ... ... ... . ... ... ... ...
[68297] chrUn_GL456396 1-21240 * | 0 chr8:57483000-57493000 10620.5 FALSE
[68298] chrUn_GL456368 1-20208 * | 0 chr8:57483000-57493000 10104.5 FALSE
[68299] chrM 1-16299 * | 0 chr8:57483000-57493000 8150.0 FALSE
[68300] chr4_JH584292_random 1-14945 * | 0 chr8:57483000-57493000 7473.0 FALSE
[68301] chr4_JH584295_random 1-1976 * | 0 chr8:57483000-57493000 988.5 FALSE
-------
seqinfo: 66 sequences from an unspecified genome; no seqlengths
My sessionInfo():
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so; LAPACK version 3.7.1
locale:
[1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=C LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=C LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] HiContacts_1.3.0 HiCExperiment_1.1.0
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.30.2 gtable_0.3.3 beeswarm_0.4.0
[4] ggplot2_3.4.2 rhdf5_2.44.0 Biobase_2.60.0
[7] lattice_0.21-8 tzdb_0.4.0 rhdf5filters_1.12.1
[10] vctrs_0.6.2 tools_4.3.0 bitops_1.0-7
[13] generics_0.1.3 stats4_4.3.0 parallel_4.3.0
[16] tibble_3.2.1 fansi_1.0.4 pkgconfig_2.0.3
[19] Matrix_1.5-4.1 S4Vectors_0.38.1 lifecycle_1.0.3
[22] GenomeInfoDbData_1.2.10 compiler_4.3.0 stringr_1.5.0
[25] munsell_0.5.0 codetools_0.2-19 InteractionSet_1.29.1
[28] vipor_0.4.5 GenomeInfoDb_1.36.0 RCurl_1.98-1.12
[31] pillar_1.9.0 crayon_1.5.2 tidyr_1.3.0
[34] BiocParallel_1.34.2 DelayedArray_0.26.3 RSpectra_0.16-1
[37] tidyselect_1.2.0 stringi_1.7.12 dplyr_1.1.2
[40] purrr_1.0.1 grid_4.3.0 colorspace_2.1-0
[43] cli_3.6.1 magrittr_2.0.3 S4Arrays_1.0.4
[46] utf8_1.2.3 withr_2.5.0 readr_2.1.4
[49] scales_1.2.1 bit64_4.0.5 ggbeeswarm_0.7.2
[52] XVector_0.40.0 matrixStats_1.0.0 bit_4.0.5
[55] hms_1.1.3 ggrastr_1.0.2 GenomicRanges_1.52.0
[58] IRanges_2.34.0 BiocIO_1.10.0 rlang_1.1.1
[61] Rcpp_1.0.10 glue_1.6.2 BiocGenerics_0.46.0
[64] vroom_1.6.3 strawr_0.0.91 R6_2.5.1
[67] Rhdf5lib_1.22.0 MatrixGenerics_1.12.2 zlibbioc_1.46.0Could you please share your sessionInfo()?
Also, I filled an issue to InteractionSet, as a hot-fix had not been included in the latest release version (1.28.0). You may have to install 1.29.1 from github: remotes::install_github("LTLA/InteractionSet") to sort all the issues (though the one you reported should be fixed in
Many thank,
I installed the InteractionSet tool many thanks!
Here my session:
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.0.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[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] SummarizedExperiment_1.28.0 Biobase_2.58.0 MatrixGenerics_1.10.0
[4] matrixStats_1.0.0 remotes_2.4.2 devtools_2.4.5
[7] usethis_2.2.0 HiCExperiment_1.1.0 rtracklayer_1.58.0
[10] ggplot2_3.4.2 HiContactsData_1.0.0 ExperimentHub_2.6.0
[13] AnnotationHub_3.6.0 BiocFileCache_2.6.1 dbplyr_2.3.2
[16] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 IRanges_2.32.0
[19] S4Vectors_0.36.2 BiocGenerics_0.44.0 HiContacts_1.3.0
loaded via a namespace (and not attached):
[1] backports_1.4.1 Hmisc_5.1-0
[3] igraph_1.4.3 lazyeval_0.2.2
[5] BiocParallel_1.32.6 digest_0.6.31
[7] ensembldb_2.22.0 htmltools_0.5.5
[9] fansi_1.0.4 magrittr_2.0.3
[11] checkmate_2.2.0 memoise_2.0.1
[13] BSgenome_1.66.3 cluster_2.1.4
[15] tzdb_0.4.0 InteractionSet_1.29.1
[17] Biostrings_2.66.0 vroom_1.6.3
[19] prettyunits_1.1.1 jpeg_0.1-10
[21] colorspace_2.1-0 blob_1.2.4
[23] rappdirs_0.3.3 xfun_0.39
[25] dplyr_1.1.2 jsonlite_1.8.5
[27] callr_3.7.3 crayon_1.5.2
[29] RCurl_1.98-1.12 VariantAnnotation_1.44.1
[31] glue_1.6.2 gtable_0.3.3
[33] zlibbioc_1.44.0 XVector_0.38.0
[35] strawr_0.0.91 DelayedArray_0.24.0
[37] pkgbuild_1.4.0 Rhdf5lib_1.20.0
[39] scales_1.2.1 DBI_1.1.3
[41] miniUI_0.1.1.1 Rcpp_1.0.10
[43] xtable_1.8-4 progress_1.2.2
[45] htmlTable_2.4.1 reticulate_1.30
[47] foreign_0.8-84 bit_4.0.5
[49] Formula_1.2-5 profvis_0.3.8
[51] htmlwidgets_1.6.2 httr_1.4.6
[53] RColorBrewer_1.1-3 ellipsis_0.3.2
[55] urlchecker_1.0.1 pkgconfig_2.0.3
[57] XML_3.99-0.14 Gviz_1.42.1
[59] nnet_7.3-19 deldir_1.0-9
[61] utf8_1.2.3 tidyselect_1.2.0
[63] rlang_1.1.1 later_1.3.1
[65] AnnotationDbi_1.60.2 BiocVersion_3.16.0
[67] munsell_0.5.0 tools_4.2.1
[69] cachem_1.0.8 cli_3.6.1
[71] generics_0.1.3 RSQLite_2.3.1
[73] evaluate_0.21 stringr_1.5.0
[75] fastmap_1.1.1 yaml_2.3.7
[77] processx_3.8.1 knitr_1.43
[79] bit64_4.0.5 fs_1.6.2
[81] purrr_1.0.1 KEGGREST_1.38.0
[83] AnnotationFilter_1.22.0 mime_0.12
[85] ggrastr_1.0.2 xml2_1.3.4
[87] biomaRt_2.54.1 compiler_4.2.1
[89] rstudioapi_0.14 beeswarm_0.4.0
[91] interactiveDisplayBase_1.36.0 filelock_1.0.2
[93] curl_5.0.1 png_0.1-8
[95] tibble_3.2.1 stringi_1.7.12
[97] ps_1.7.5 desc_1.4.2
[99] GenomicFeatures_1.50.4 lattice_0.21-8
[101] ProtGenerics_1.30.0 Matrix_1.5-4.1
[103] vctrs_0.6.2 rhdf5filters_1.10.1
[105] pillar_1.9.0 GenomicInteractions_1.32.0
[107] lifecycle_1.0.3 BiocManager_1.30.21
[109] data.table_1.14.8 bitops_1.0-7
[111] httpuv_1.6.11 R6_2.5.1
[113] BiocIO_1.8.0 latticeExtra_0.6-30
[115] promises_1.2.0.1 gridExtra_2.3
[117] vipor_0.4.5 sessioninfo_1.2.2
[119] codetools_0.2-19 dichromat_2.0-0.1
[121] pkgload_1.3.2 rhdf5_2.42.1
[123] rprojroot_2.0.3 rjson_0.2.21
[125] withr_2.5.0 GenomicAlignments_1.34.1
[127] Rsamtools_2.14.0 GenomeInfoDbData_1.2.9
[129] parallel_4.2.1 hms_1.1.3
[131] grid_4.2.1 rpart_4.1.19
[133] tidyr_1.3.0 rmarkdown_2.22
[135] biovizBase_1.46.0 shiny_1.7.4
[137] base64enc_0.1-3 ggbeeswarm_0.7.2
[139] interp_1.1-4 restfulr_0.0.15
This is odd. For troubleshooting, could you start a new R instance, paste the following commands and send me the output?
library(HiCExperiment)
library(GenomicRanges)
hic <- import('GSE161259_ES_chr8_55400000_59200000_MAPQ30.40kb.cool')
##
print(HiContacts::virtual4C)
HiContacts::virtual4C(hic, GRanges("chr8:57483000-57493000"))
##
gis <- interactions(hic)
cm <- Matrix::as.matrix(gi2cm(gis, 'balanced'))
cm <- base::as.matrix(cm)
regions <- regions(gis)
regions_in_viewpoint <- seq_along(regions) %in% queryHits(
findOverlaps(regions, GRanges("chr8:57483000-57493000"))
)
score <- cm[, regions_in_viewpoint]
##
table(regions_in_viewpoint)
head(score)Thanks