Marc-Ruebsam
commented
2 years ago The data seems to load without problems in the latest Bioconductor version of YAPSA. Please update your package and report any further errors there: https://support.bioconductor.org/tag/YAPSA/
> suppressPackageStartupMessages(library("YAPSA"))
> data(GenomeOfNl_raw)
> head(GenomeOfNl_raw)
CHROM POS ID REF ALT QUAL FILTER INFO
32 2 12320 rs147364131 AAT A . PASS AC=31;AF=0.031;AN=998;DB;NUMALT=1;set=INDEL
53 2 13613 . AG A . PASS AC=3;AF=3.006e-03;AN=998;NUMALT=1;set=INDEL
92 2 17012 rs144550470 TAAAG T . PASS AC=6;AF=6.012e-03;AN=998;DB;NUMALT=1;set=INDEL
94 2 17128 rs140420760 T TG . PASS AC=1;AF=1.002e-03;AN=998;DB;NUMALT=1;set=INDEL
95 2 17142 . G GA . PASS AC=9;AF=9.018e-03;AN=998;NUMALT=1;set=INDEL
96 2 17151 . TCAC T . PASS AC=1;AF=1.002e-03;AN=998;NUMALT=1;set=INDEL> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /home/ruebsam/.conda/envs/bioconductor_yapsa/lib/libopenblasp-r0.3.20.so
locale:
[1] C
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] YAPSA_1.19.0 Biobase_2.54.0 ggplot2_3.3.6 GenomicRanges_1.46.1 GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.3 BiocGenerics_0.40.0
loaded via a namespace (and not attached):
[1] backports_1.4.1 circlize_0.4.15 Hmisc_4.7-0 corrplot_0.92 NMF_0.21.0 BiocFileCache_2.2.0
[7] plyr_1.8.7 lazyeval_0.2.2 splines_4.1.3 BiocParallel_1.28.3 gridBase_0.4-7 gtrellis_1.26.0
[13] digest_0.6.29 foreach_1.5.2 ensembldb_2.18.1 htmltools_0.5.2 viridis_0.6.2 fansi_1.0.3
[19] magrittr_2.0.3 checkmate_2.1.0 memoise_2.0.1 BSgenome_1.62.0 cluster_2.1.3 doParallel_1.0.17
[25] ComplexHeatmap_2.10.0 Biostrings_2.62.0 matrixStats_0.62.0 limSolve_1.5.6 ggbio_1.42.0 lpSolve_5.6.15
[31] prettyunits_1.1.1 jpeg_0.1-9 colorspace_2.0-3 blob_1.2.3 rappdirs_0.3.3 xfun_0.31
[37] dplyr_1.0.9 crayon_1.5.1 RCurl_1.98-1.6 graph_1.72.0 SomaticSignatures_2.30.0 survival_3.3-1
[43] VariantAnnotation_1.40.0 iterators_1.0.14 glue_1.6.2 registry_0.5-1 gtable_0.3.0 zlibbioc_1.40.0
[49] XVector_0.34.0 GetoptLong_1.0.5 DelayedArray_0.20.0 shape_1.4.6 scales_1.2.0 rngtools_1.5.2
[55] DBI_1.1.2 GGally_2.1.2 Rcpp_1.0.8.3 xtable_1.8-4 viridisLite_0.4.0 progress_1.2.2
[61] htmlTable_2.4.0 clue_0.3-60 proxy_0.4-26 foreign_0.8-82 bit_4.0.4 OrganismDbi_1.36.0
[67] PMCMR_4.4 Formula_1.2-4 htmlwidgets_1.5.4 httr_1.4.3 RColorBrewer_1.1-3 ellipsis_0.3.2
[73] pkgconfig_2.0.3 reshape_0.8.9 XML_3.99-0.9 nnet_7.3-17 dbplyr_2.2.0 utf8_1.2.2
[79] tidyselect_1.1.2 rlang_1.0.2 reshape2_1.4.4 AnnotationDbi_1.56.1 munsell_0.5.0 tools_4.1.3
[85] cachem_1.0.6 cli_3.3.0 generics_0.1.2 RSQLite_2.2.8 stringr_1.4.0 fastmap_1.1.0
[91] yaml_2.3.5 knitr_1.39 bit64_4.0.5 purrr_0.3.4 KEGGREST_1.34.0 AnnotationFilter_1.18.0
[97] dendextend_1.15.2 RBGL_1.70.0 pracma_2.3.8 xml2_1.3.3 biomaRt_2.50.0 compiler_4.1.3
[103] rstudioapi_0.13 beeswarm_0.4.0 filelock_1.0.2 curl_4.3.2 png_0.1-7 tibble_3.1.7
[109] stringi_1.7.6 GenomicFeatures_1.46.1 lattice_0.20-45 ProtGenerics_1.26.0 Matrix_1.4-1 vctrs_0.4.1
[115] pillar_1.7.0 lifecycle_1.0.1 BiocManager_1.30.18 GlobalOptions_0.1.2 data.table_1.14.2 bitops_1.0-7
[121] rtracklayer_1.54.0 pcaMethods_1.86.0 R6_2.5.1 BiocIO_1.4.0 latticeExtra_0.6-29 gridExtra_2.3
[127] vipor_0.4.5 codetools_0.2-18 dichromat_2.0-0.1 MASS_7.3-57 assertthat_0.2.1 SummarizedExperiment_1.24.0
[133] pkgmaker_0.32.2 rjson_0.2.21 withr_2.5.0 GenomicAlignments_1.30.0 Rsamtools_2.10.0 GenomeInfoDbData_1.2.7
[139] parallel_4.1.3 hms_1.1.1 quadprog_1.5-8 rpart_4.1.16 BSgenome.Hsapiens.UCSC.hg19_1.4.3 MatrixGenerics_1.6.0
[145] biovizBase_1.42.0 base64enc_0.1-3 ggbeeswarm_0.6.0 restfulr_0.0.14
I could not find the indel dataset in your "data" repository. It's not in the package as well. Where could I find it?