jmw86069 / jampack Goto Github PK

Hello jampack team,

I had download jampack, splicejam, ferrisdata (great work by the way) and all dependencies to try to apply it to my data, but I got an error message in the gene2gg function. And I need some advice on how to solve it.

library(splicejam)
library(jampack)
data(test_exon_wide_gr);
test_flatExonsByGene <- GenomicRanges::split(test_exon_wide_gr,
GenomicRanges::values(test_exon_wide_gr)[,"gene_name"]);
gene2gg(gene="TestGene1", flatExonsByGene=test_flatExonsByGene);

with the error message:

gene2gg(gene="TestGene1", flatExonsByGene=test_flatExonsByGene);
Error in FUN(X[[i]], ...) :
no method or default for coercing “CompressedGRangesList” to “GRanges”

and my session info:

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggforce_0.3.2 ggplot2_3.3.3 jampack_0.0.21.900 splicejam_0.0.60.900 jamma_0.0.15.900
[6] colorjam_0.0.18.900 jamba_0.0.62.900
loaded via a namespace (and not attached):
[1] httr_1.4.2 pkgload_1.2.0 tidyr_1.1.2
[4] jsonlite_1.7.2 viridisLite_0.3.0 shiny_1.6.0
[7] assertthat_0.2.1 stats4_4.0.3 GenomeInfoDbData_1.2.4
[10] remotes_2.2.0 sessioninfo_1.1.1 pillar_1.5.1
[13] glue_1.4.2 digest_0.6.27 polyclip_1.10-0
[16] GenomicRanges_1.42.0 promises_1.2.0.1 XVector_0.30.0
[19] colorspace_2.0-0 htmltools_0.5.1.1 httpuv_1.5.5
[22] pkgconfig_2.0.3 devtools_2.3.2 zlibbioc_1.36.0
[25] purrr_0.3.4 xtable_1.8-4 scales_1.1.1
[28] processx_3.4.5 tweenr_1.0.1 later_1.1.0.1
[31] tibble_3.1.0 farver_2.1.0 generics_0.1.0
[34] IRanges_2.24.1 usethis_2.0.1 ellipsis_0.3.1
[37] cachem_1.0.4 withr_2.4.1 BiocGenerics_0.36.0
[40] lazyeval_0.2.2 cli_2.3.1 magrittr_2.0.1
[43] crayon_1.4.1 mime_0.10 memoise_2.0.0.9000
[46] ps_1.5.0 fs_1.5.0 fansi_0.4.2
[49] MASS_7.3-53.1 pkgbuild_1.2.0 shinydashboard_0.7.1
[52] tools_4.0.3 data.table_1.14.0 prettyunits_1.1.1
[55] lifecycle_1.0.0 plotly_4.9.3 S4Vectors_0.28.1
[58] munsell_0.5.0 callr_3.5.1 compiler_4.0.3
[61] GenomeInfoDb_1.26.2 rlang_0.4.10 grid_4.0.3
[64] RCurl_1.98-1.2 shinydashboardPlus_2.0.0.9000 rstudioapi_0.13
[67] htmlwidgets_1.5.3 bitops_1.0-6 shinyWidgets_0.5.7
[70] testthat_3.0.2 gtable_0.3.0 DBI_1.1.1
[73] curl_4.3 R6_2.5.0 dplyr_1.0.4
[76] fastmap_1.1.0 utf8_1.1.4 rprojroot_2.0.2
[79] desc_1.2.0 parallel_4.0.3 Rcpp_1.0.6
[82] vctrs_0.3.6 tidyselect_1.1.0

Thank you in advance.