Looks like that you are trying to annotate peaks. If that is the case, you might want to try the function annotatePeakInBatch in the ChIPpeakAnno package http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html. Best regards, Julie Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User chitsazanalex<https: support.bioconductor.org="" u="" 11765=""/> wrote Question: DistanceToNearest Not giving nearest Range<https: support.bioconductor.org="" p="" 104015=""/>: I'm having trouble why the order of my subject is calling two different nearest cordinates. One is obviously closer, but for some reason it's chosing the first one rather than the actual nearest one. How can I fix this? Thanks! Here is my code and a session_info() printout. > ALL_merged_summits.gr["All_merged_peak_37393"] GRanges object with 1 range and 4 metadata columns: seqnames ranges strand | Peak Pileup Gene <rle> <iranges> <rle> | <factor> <numeric> <character> All_merged_peak_37393 Chr04 [9853878, 9854277] * | All_merged_peak_37393 3.1272 Xetrov90010392m.g DistanceToTSS <numeric> All_merged_peak_37393 -59404 ------- seqinfo: 3748 sequences from an unspecified genome; no seqlengths > TSS[c("Xetrov90010392m.g", "pax6")] GRanges object with 2 ranges and 0 metadata columns: seqnames ranges strand <rle> <iranges> <rle> Xetrov90010392m.g Chr04 [9794473, 9794473] - pax6 Chr04 [9859219, 9859219] + ------- seqinfo: 1515 sequences from an unspecified genome; no seqlengths > distanceToNearestALL_merged_summits.gr["All_merged_peak_37393"], TSS[c("Xetrov90010392m.g", "pax6")]) Hits object with 1 hit and 1 metadata column: queryHits subjectHits | distance <integer> <integer> | <integer> [1] 1 1 | 59404 ------- queryLength: 1 / subjectLength: 2 > distanceToNearestALL_merged_summits.gr["All_merged_peak_37393"], TSS[c("pax6", "Xetrov90010392m.g")]) Hits object with 1 hit and 1 metadata column: queryHits subjectHits | distance <integer> <integer> | <integer> [1] 1 1 | 4941 ------- queryLength: 1 / subjectLength: 2 > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] topGO_2.28.0 SparseM_1.77 GO.db_3.4.1 graph_1.54.0 AnnotationDbi_1.38.2 [6] Biobase_2.36.2 biomaRt_2.32.1 VennDiagram_1.6.17 futile.logger_1.4.3 RColorBrewer_1.1-2 [11] knitr_1.17 ggplot2_2.2.1 GenomicRanges_1.28.6 GenomeInfoDb_1.12.3 IRanges_2.10.5 [16] S4Vectors_0.14.7 BiocGenerics_0.22.1 kableExtra_0.6.1 edgeR_3.18.1 limma_3.32.10 loaded via a namespace (and not attached): [1] httr_1.3.1 tidyr_0.7.2 splines_3.4.2 bit64_0.9-7 [5] jsonlite_1.5 viridisLite_0.2.0 modelr_0.1.1 assertthat_0.2.0 [9] highr_0.6 blob_1.1.0 GenomeInfoDbData_0.99.0 cellranger_1.1.0 [13] RSQLite_2.0 backports_1.1.1 lattice_0.20-35 glue_1.2.0 [17] digest_0.6.12 XVector_0.16.0 rvest_0.3.2 colorspace_1.3-2 [21] htmltools_0.3.6 plyr_1.8.4 psych_1.7.8 XML_3.98-1.9 [25] pkgconfig_2.0.1 broom_0.4.2 haven_1.1.0 zlibbioc_1.22.0 [29] purrr_0.2.4 scales_0.5.0 tibble_1.3.4 lazyeval_0.2.1 [33] mnormt_1.5-5 magrittr_1.5 crayon_1.3.4 readxl_1.0.0 [37] memoise_1.1.0 evaluate_0.10.1 nlme_3.1-131 forcats_0.2.0 [41] xml2_1.1.1 foreign_0.8-69 tools_3.4.2 hms_0.3 [45] matrixStats_0.52.2 stringr_1.2.0 munsell_0.4.3 locfit_1.5-9.1 [49] lambda.r_1.2 bindrcpp_0.2 compiler_3.4.2 rlang_0.1.4 [53] RCurl_1.95-4.8 rstudioapi_0.7 bitops_1.0-6 rmarkdown_1.6 [57] gtable_0.2.0 DBI_0.7 reshape2_1.4.2 R6_2.2.2 [61] lubridate_1.7.1 dplyr_0.7.4 bit_1.1-12 bindr_0.1 [65] rprojroot_1.2 futile.options_1.0.0 readr_1.1.1 stringi_1.1.5 [69] Rcpp_0.12.13 > ________________________________ Post tags: GRanges, distancetonearest You may reply via email or visit DistanceToNearest Not giving nearest Range