Closed ckrushton closed 2 years ago
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /gsc/software/linux-x86_64-centos7/R-4.1.3/lib64/R/lib/libRblas.so
LAPACK: /gsc/software/linux-x86_64-centos7/R-4.1.3/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GAMBLR_0.0.0.9500 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.9 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.7
[9] ggplot2_3.3.6 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] readxl_1.4.0 backports_1.4.1 circlize_0.4.15 workflowr_1.7.0 RCircos_1.2.2
[6] plyr_1.8.7 splines_4.1.3 BiocParallel_1.28.3 usethis_2.1.5 GenomeInfoDb_1.30.1
[11] digest_0.6.29 foreach_1.5.2 htmltools_0.5.2 fansi_1.0.3 magrittr_2.0.3
[16] metaviz_0.3.1 memoise_2.0.1 cgdsr_1.3.0 cluster_2.1.3 config_0.3.1
[21] doParallel_1.0.17 tzdb_0.3.0 limma_3.50.3 remotes_2.4.2 ComplexHeatmap_2.10.0
[26] Biostrings_2.62.0 modelr_0.1.8 matrixStats_0.62.0 vroom_1.5.7 prettyunits_1.1.1
[31] colorspace_2.0-3 blob_1.2.3 rvest_1.0.2 ggrepel_0.9.1 xfun_0.31
[36] haven_2.5.0 callr_3.7.0 crayon_1.5.1 RCurl_1.98-1.7 jsonlite_1.8.0
[41] GEOquery_2.62.2 survival_3.3-1 iterators_1.0.14 glue_1.6.2 SRAdb_1.56.0
[46] gtable_0.3.0 zlibbioc_1.40.0 XVector_0.34.0 GetoptLong_1.0.5 DelayedArray_0.20.0
[51] car_3.1-0 pkgbuild_1.3.1 shape_1.4.6 BiocGenerics_0.40.0 abind_1.4-5
[56] scales_1.2.0 DBI_1.1.3 rstatix_0.7.0 ggthemes_4.2.4 Rcpp_1.0.8.3
[61] clue_0.3-61 bit_4.0.4 stats4_4.1.3 httr_1.4.3 htmlwidgets_1.5.4
[66] RColorBrewer_1.1-3 ellipsis_0.3.2 pkgconfig_2.0.3 XML_3.99-0.10 R.methodsS3_1.8.2
[71] dbplyr_2.2.0 utf8_1.2.2 RMariaDB_1.2.2 later_1.3.0 tidyselect_1.1.2
[76] rlang_1.0.2 reshape2_1.4.4 cellranger_1.1.0 munsell_0.5.0 tools_4.1.3
[81] cachem_1.0.6 cli_3.3.0 generics_0.1.2 devtools_2.4.3 broom_0.8.0
[86] evaluate_0.15 fastmap_1.1.0 yaml_2.3.5 knitr_1.39 processx_3.6.1
[91] bit64_4.0.5 fs_1.5.2 R.oo_1.25.0 xml2_1.3.3 brio_1.1.3
[96] compiler_4.1.3 rstudioapi_0.13 curl_4.3.2 png_0.1-7 testthat_3.1.4
[101] maftools_2.10.05 ggsignif_0.6.3 reprex_2.0.1 stringi_1.7.6 ps_1.7.1
[106] desc_1.4.1 lattice_0.20-45 Matrix_1.4-1 ggsci_2.9 vctrs_0.4.1
[111] pillar_1.7.0 lifecycle_1.0.1 g3viz_1.1.4 GlobalOptions_0.1.2 data.table_1.14.2
[116] cowplot_1.1.1 bitops_1.0-7 httpuv_1.6.5 rtracklayer_1.54.0 GenomicRanges_1.46.1
[121] R6_2.5.1 BiocIO_1.4.0 promises_1.2.0.1 IRanges_2.28.0 sessioninfo_1.2.2
[126] codetools_0.2-18 assertthat_0.2.1 pkgload_1.2.4 SummarizedExperiment_1.24.0 rprojroot_2.0.3
[131] rjson_0.2.21 withr_2.5.0 GenomicAlignments_1.30.0 Rsamtools_2.10.0 S4Vectors_0.32.4
[136] GenomeInfoDbData_1.2.7 parallel_4.1.3 hms_1.1.1 grid_4.1.3 rmarkdown_2.14
[141] MatrixGenerics_1.6.0 carData_3.0-5 ggpubr_0.4.0 lubridate_1.8.0 Biobase_2.54.0
[146] restfulr_0.0.15 ```
@mattssca already fixed this issue. Here's how I run it and it works on my branch. Waiting for that PR to be merged, unfortunately.
all_dlbcl_genome_ashm = get_ssm_by_regions(regions_bed=regions_bed,seq_type="genome",streamlined = F)
The PR with a fix for this has now been merged into Master
Running
get_ssm_by_regions(grch37_ashm_regions)
yields the following dataframe:For some reason, this function is only returning variants upstream of MYC, and assigning them to (seemingly) ALL regions provided