Rbind error during permutations #72
Description
Hello!
Thanks for the tool!
I am encountering an error that seems to be recurrent but should have been fixed according to the forums.
I am using dmrseq_1.26.0 , installed from BiocManager and having the following error (testCovariate is multi-factor):
blocks <- dmrseq(bs=bsseq_obj,
cutoff = 0.05,
testCovariate="Genotype",
adjustCovariate = 'Replicate',
block = TRUE,
minInSpan = 500,
bpSpan = 5e4,
maxGapSmooth = 1e6,
maxGap = 5e3)
Beginning permutation 5
...Chromosome chr1: Smoothed (0.04 min). 430 regions scored (0.47 min).
...Chromosome chr10: Smoothed (0.05 min). 272 regions scored (0.25 min).
...Chromosome chr11: Smoothed (0.02 min). Error in rbind(deparse.level, ...) :
numbers of columns of arguments do not match
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Red Hat Enterprise Linux 8.8 (Ootpa)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so; LAPACK version 3.9.0
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: Europe/Rome
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocParallel_1.40.2 data.table_1.17.0 RColorBrewer_1.1-3 dmrseq_1.26.0
[5] bsseq_1.42.0 SummarizedExperiment_1.36.0 Biobase_2.66.0 MatrixGenerics_1.18.1
[9] matrixStats_1.5.0 GenomicRanges_1.58.0 GenomeInfoDb_1.42.3 IRanges_2.40.1
[13] S4Vectors_0.44.0 BiocGenerics_0.52.0
loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-9 permute_0.9-7 rlang_1.1.6
[5] magrittr_2.0.3 compiler_4.4.0 RSQLite_2.3.9 GenomicFeatures_1.58.0
[9] DelayedMatrixStats_1.28.1 png_0.1-8 vctrs_0.6.5 reshape2_1.4.4
[13] stringr_1.5.1 pkgconfig_2.0.3 crayon_1.5.3 fastmap_1.2.0
[17] dbplyr_2.5.0 XVector_0.46.0 Rsamtools_2.22.0 tzdb_0.5.0
[21] UCSC.utils_1.2.0 bit_4.6.0 zlibbioc_1.52.0 cachem_1.1.0
[25] jsonlite_2.0.0 blob_1.2.4 rhdf5filters_1.18.1 DelayedArray_0.32.0
[29] Rhdf5lib_1.28.0 parallel_4.4.0 R6_2.6.1 stringi_1.8.7
[33] limma_3.62.2 rtracklayer_1.66.0 iterators_1.0.14 Rcpp_1.0.14
[37] R.utils_2.13.0 readr_2.1.5 splines_4.4.0 Matrix_1.7-0
[41] tidyselect_1.2.1 abind_1.4-8 yaml_2.3.10 codetools_0.2-20
[45] curl_6.2.2 doRNG_1.8.6.2 lattice_0.22-6 tibble_3.2.1
[49] regioneR_1.38.0 plyr_1.8.9 KEGGREST_1.46.0 BiocFileCache_2.14.0
[53] Biostrings_2.74.1 pillar_1.10.2 BiocManager_1.30.25 filelock_1.0.3
[57] rngtools_1.5.2 foreach_1.5.2 generics_0.1.3 RCurl_1.98-1.17
[61] BiocVersion_3.20.0 hms_1.1.3 ggplot2_3.5.2 sparseMatrixStats_1.18.0
[65] munsell_0.5.1 scales_1.3.0 bumphunter_1.48.0 gtools_3.9.5
[69] glue_1.8.0 tools_4.4.0 AnnotationHub_3.14.0 BiocIO_1.16.0
[73] BSgenome_1.74.0 locfit_1.5-9.12 GenomicAlignments_1.42.0 XML_3.99-0.18
[77] rhdf5_2.50.2 grid_4.4.0 AnnotationDbi_1.68.0 colorspace_2.1-1
[81] nlme_3.1-164 GenomeInfoDbData_1.2.13 HDF5Array_1.34.0 restfulr_0.0.15
[85] annotatr_1.32.0 cli_3.6.4 rappdirs_0.3.3 S4Arrays_1.6.0
[89] dplyr_1.1.4 gtable_0.3.6 outliers_0.15 R.methodsS3_1.8.2
[93] digest_0.6.37 SparseArray_1.6.2 rjson_0.2.23 memoise_2.0.1
[97] R.oo_1.27.0 lifecycle_1.0.4 httr_1.4.7 statmod_1.5.0
[101] bit64_4.6.0-1
This error did not occur when using just a subset of the regions to test.
Can you please advise on how to fix it?
Thank you!!