Open rosaranli opened 4 years ago
Thanks for catching and reporting this bug. It has been addressed in commit https://github.com/JEFworks/HoneyBADGER/commit/b3648e766d2e885910b5c0758b18c62a63ca3471
Thank you so much for looking into the case and sorry for commenting on the closed issue. I reran the updated package and still found an error in summarizeResults. If I use the expression data provided by the package and follow the tutorial exactly, there is an error when I ran
hb$calcGexpCnvBoundaries(init=TRUE, verbose=FALSE) ERROR: Error: subscript contains invalid names NULL
It was not there before and it showed different identified CNV regions as shown on the website. The regions are
print(regions.genes) GRanges object with 5 ranges and 0 metadata columns: seqnames ranges strand
No problem at all. Thanks for the report. Let me reopen this issue for now so I can remember to address it when I get the chance.
Hi,
I followed the "Getting Started" tutorial on the website to identify CNVs from expression data. I have no problem runing the functions until I run summarizeResults. The error is Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
Could you please advise what could cause the error? Thank you so much.
sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.8 (Final)
Matrix products: default BLAS: /data/nephron/ranli/tools/lib64/R/lib/libRblas.so LAPACK: /data/nephron/ranli/tools/lib64/R/lib/libRlapack.so
locale: [1] C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] rjags_4-8 coda_0.19-3 biomaRt_2.40.1 HoneyBADGER_0.1
loaded via a namespace (and not attached): [1] progress_1.2.2 tidyselect_0.2.5 purrr_0.3.2
[4] reshape2_1.4.3 lattice_0.20-38 colorspace_1.4-1
[7] vctrs_0.2.0 stats4_3.6.0 blob_1.2.0
[10] XML_3.98-1.20 rlang_0.4.0 pillar_1.4.2
[13] glue_1.3.1 DBI_1.0.0 BiocGenerics_0.30.0
[16] bit64_0.9-7 GenomeInfoDbData_1.2.1 plyr_1.8.4
[19] zlibbioc_1.30.0 stringr_1.4.0 munsell_0.5.0
[22] gtable_0.3.0 caTools_1.17.1.2 memoise_1.1.0
[25] Biobase_2.44.0 HiddenMarkov_1.8-11 IRanges_2.18.1
[28] GenomeInfoDb_1.20.0 parallel_3.6.0 curl_3.3
[31] AnnotationDbi_1.46.0 Rcpp_1.0.1 scales_1.0.0
[34] backports_1.1.4 S4Vectors_0.22.0 XVector_0.24.0
[37] bit_1.1-14 gridExtra_2.3 ggplot2_3.2.0
[40] hms_0.5.0 digest_0.6.20 stringi_1.4.3
[43] dplyr_0.8.3 GenomicRanges_1.36.0 grid_3.6.0
[46] tools_3.6.0 bitops_1.0-6 magrittr_1.5
[49] lazyeval_0.2.2 RCurl_1.95-4.12 tibble_2.1.3
[52] RSQLite_2.1.1 crayon_1.3.4 pkgconfig_2.0.2
[55] zeallot_0.1.0 prettyunits_1.0.2 assertthat_0.2.1
[58] httr_1.4.0 R6_2.4.0 compiler_3.6.0