Does anyone know where to get Arabidopsis thaliana's BED file for genome annotations?
I want to get one for Methylkit readTranscriptFeatures function to annotate my differential methylated region. I looked at the sample BED file in Methylkit tutorial refseq.hg18.bed.txt and I would like to make a similar file for Arabidopsis TAIR10. Here is my customized file for Arabidopsis.
Unfortunately, I encountered the following issues after running my code for Methylkit
gene.obj=readTranscriptFeatures("D:/Final_bed_file_for_Arabidopsis_genome_annotation.bed.txt", remove.unusual = FALSE)
Reading the table...
Calculating intron coordinates...
Error in `$<-.data.frame`(`*tmp*`, "V3", value = c(30425977L, 30426268L, :
replacement has 208215 rows, data has 205647
In addition: Warning messages:
1: In cbind(...) :
number of rows of result is not a multiple of vector length (arg 2)
2: In rep.ref$V2 + b.start.size[, 1] :
longer object length is not a multiple of shorter object length
I tried using BED file from UCSC from the table browser, but the file does not contain exon information, therefore not useful to me. I guess the issue lies in how the source code defines b.start.size. Any forms of help is appreciated!
Here is my session info:
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: Asia/Shanghai
tzcode source: internal
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] genomation_1.32.0 methylKit_1.26.0 GenomicFeatures_1.52.2 AnnotationDbi_1.62.2
[5] Biobase_2.60.0 GenomicRanges_1.52.0 GenomeInfoDb_1.36.1 IRanges_2.34.1
[9] S4Vectors_0.38.1 BiocGenerics_0.46.0
loaded via a namespace (and not attached):
[1] splines_4.3.1 later_1.3.1 BiocIO_1.10.0
[4] bitops_1.0-7 ggplotify_0.1.1 filelock_1.0.2
[7] R.oo_1.25.0 tibble_3.2.1 polyclip_1.10-4
[10] XML_3.99-0.14 lifecycle_1.0.3 doParallel_1.0.17
[13] vroom_1.6.3 processx_3.8.2 lattice_0.21-8
[16] MASS_7.3-60 magrittr_2.0.3 limma_3.56.2
[19] plotrix_3.8-2 yaml_2.3.7 remotes_2.4.2.1
[22] httpuv_1.6.11 sessioninfo_1.2.2 pkgbuild_1.4.2
[25] cowplot_1.1.1 DBI_1.1.3 RColorBrewer_1.1-3
[28] abind_1.4-5 pkgload_1.3.2.1 zlibbioc_1.46.0
[31] R.utils_2.12.2 purrr_1.0.1 ggraph_2.1.0
[34] RCurl_1.98-1.12 yulab.utils_0.0.6 tweenr_2.0.2
[37] rappdirs_0.3.3 circlize_0.4.15 GenomeInfoDbData_1.2.10
[40] enrichplot_1.20.0 ggrepel_0.9.3 tidytree_0.4.4
[43] DelayedArray_0.26.7 colorRamp2_0.1.0 codetools_0.2-19
[46] DOSE_3.26.1 xml2_1.3.5 ggforce_0.4.1
[49] tidyselect_1.2.0 shape_1.4.6 aplot_0.1.10
[52] farver_2.1.1 viridis_0.6.4 matrixStats_1.0.0
[55] BiocFileCache_2.8.0 GenomicAlignments_1.36.0 jsonlite_1.8.7
[58] GetoptLong_1.0.5 ellipsis_0.3.2 tidygraph_1.2.3
[61] iterators_1.0.14 bbmle_1.0.25 foreach_1.5.2
[64] tools_4.3.1 progress_1.2.2 treeio_1.24.3
[67] Rcpp_1.0.11 glue_1.6.2 gridExtra_2.3
[70] qvalue_2.32.0 MatrixGenerics_1.12.3 usethis_2.2.2
[73] dplyr_1.1.2 numDeriv_2016.8-1.1 withr_2.5.0
[76] BiocManager_1.30.21.1 fastmap_1.1.1 fansi_1.0.4
[79] callr_3.7.3 digest_0.6.33 R6_2.5.1
[82] mime_0.12 gridGraphics_0.5-1 seqPattern_1.32.0
[85] colorspace_2.1-0 GO.db_3.17.0 gtools_3.9.4
[88] biomaRt_2.56.1 RSQLite_2.3.1 R.methodsS3_1.8.2
[91] utf8_1.2.3 tidyr_1.3.0 generics_0.1.3
[94] data.table_1.14.8 rtracklayer_1.60.0 S4Arrays_1.0.5
[97] prettyunits_1.1.1 graphlayouts_1.0.0 httr_1.4.6
[100] htmlwidgets_1.6.2 scatterpie_0.2.1 pkgconfig_2.0.3
[103] gtable_0.3.3 blob_1.2.4 impute_1.74.1
[106] ComplexHeatmap_2.16.0 XVector_0.40.0 clusterProfiler_4.8.2
[109] shadowtext_0.1.2 htmltools_0.5.5 profvis_0.3.8
[112] fgsea_1.26.0 clue_0.3-64 scales_1.2.1
[115] png_0.1-8 ggfun_0.1.1 rstudioapi_0.15.0
[118] tzdb_0.4.0 reshape2_1.4.4 rjson_0.2.21
[121] coda_0.19-4 nlme_3.1-162 curl_5.0.1
[124] bdsmatrix_1.3-6 cachem_1.0.8 GlobalOptions_0.1.2
[127] stringr_1.5.0 KernSmooth_2.23-22 parallel_4.3.1
[130] miniUI_0.1.1.1 HDO.db_0.99.1 restfulr_0.0.15
[133] pillar_1.9.0 vctrs_0.6.3 urlchecker_1.0.1
[136] promises_1.2.0.1 dbplyr_2.3.3 xtable_1.8-4
[139] cluster_2.1.4 readr_2.1.4 mvtnorm_1.2-2
[142] cli_3.6.1 compiler_4.3.1 Rsamtools_2.16.0
[145] rlang_1.1.1 crayon_1.5.2 mclust_6.0.0
[148] emdbook_1.3.13 ps_1.7.5 plyr_1.8.8
[151] fs_1.6.2 stringi_1.7.12 gridBase_0.4-7
[154] viridisLite_0.4.2 BiocParallel_1.34.2 munsell_0.5.0
[157] Biostrings_2.68.1 lazyeval_0.2.2 devtools_2.4.5
[160] GOSemSim_2.26.1 Matrix_1.6-0 BSgenome_1.68.0
[163] hms_1.1.3 patchwork_1.1.2 bit64_4.0.5
[166] ggplot2_3.4.2 KEGGREST_1.40.0 shiny_1.7.4.1
[169] fastseg_1.46.0 SummarizedExperiment_1.30.2 igraph_1.5.0.1
[172] memoise_2.0.1 ggtree_3.8.2 fastmatch_1.1-3
[175] bit_4.0.5 downloader_0.4 ape_5.7-1
[178] gson_0.1.0