Open ConYel opened 2 years ago
I try to use reduce_ranges on the example found in https://bioconductor.github.io/BiocWorkshops/fluent-genomic-data-analysis-with-plyranges.html but I get a strange output:
library(plyranges, quietly = TRUE) genes <- data.frame(seqnames = "VI", start = c(3322, 3030, 1437, 5066, 6426, 836), end = c(3846, 3338, 2615, 5521, 7565, 1363), strand = c("-", "-", "-", "+", "+", "+"), gene_id=c("YFL064C", "YFL065C", "YFL066C", "YFL063W", "YFL062W", "YFL067W"), stringsAsFactors = FALSE) gr <- as_granges(genes) gr %>% reduce_ranges(gene_id = List(gene_id)) GRanges object with 5 ranges and 1 metadata column: seqnames ranges strand | gene_id <Rle> <IRanges> <Rle> | <List> [1] VI 836-1363 + | YFL067W,YFL063W,YFL062W,... [2] VI 5066-5521 + | YFL067W,YFL063W,YFL062W,... [3] VI 6426-7565 + | YFL067W,YFL063W,YFL062W,... [4] VI 1437-2615 - | YFL067W,YFL063W,YFL062W,... [5] VI 3030-3846 - | YFL067W,YFL063W,YFL062W,... ------- seqinfo: 1 sequence from an unspecified genome; no seqlengths
options(width = 120) sessioninfo::session_info() ─ Session info setting value version R version 4.1.0 (2021-05-18) os Ubuntu 20.04.2 LTS system x86_64, linux-gnu ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Etc/UTC date 2021-10-18 ─ Packages package * version date lib source assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.1.0) backports 1.2.1 2020-12-09 [1] RSPM (R 4.1.0) Biobase 2.53.0 2021-05-19 [1] Bioconductor BiocGenerics * 0.39.1 2021-06-08 [1] Bioconductor BiocIO 1.3.0 2021-05-19 [1] Bioconductor BiocParallel 1.27.2 2021-07-12 [1] Bioconductor Biostrings 2.61.1 2021-06-04 [1] Bioconductor bit 4.0.4 2020-08-04 [1] RSPM (R 4.1.0) bit64 4.0.5 2020-08-30 [1] RSPM (R 4.1.0) bitops 1.0-7 2021-04-24 [1] RSPM (R 4.1.0) broom 0.7.9 2021-07-27 [1] RSPM (R 4.1.0) cellranger 1.1.0 2016-07-27 [1] RSPM (R 4.1.0) cli 3.0.1 2021-07-17 [1] RSPM (R 4.1.0) colorspace 2.0-2 2021-06-24 [1] RSPM (R 4.1.0) crayon 1.4.1 2021-02-08 [1] RSPM (R 4.1.0) DBI 1.1.1 2021-01-15 [1] RSPM (R 4.1.0) dbplyr 2.1.1 2021-04-06 [1] RSPM (R 4.1.0) DelayedArray 0.19.1 2021-06-25 [1] Bioconductor digest 0.6.27 2020-10-24 [1] RSPM (R 4.1.0) dplyr * 1.0.7 2021-06-18 [1] RSPM (R 4.1.0) ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.1.0) evaluate 0.14 2019-05-28 [1] RSPM (R 4.1.0) fansi 0.5.0 2021-05-25 [1] RSPM (R 4.1.0) forcats * 0.5.1 2021-01-27 [1] RSPM (R 4.1.0) fs 1.5.0 2020-07-31 [1] RSPM (R 4.1.0) generics 0.1.0 2020-10-31 [1] RSPM (R 4.1.0) GenomeInfoDb * 1.29.3 2021-07-01 [1] Bioconductor GenomeInfoDbData 1.2.6 2021-08-04 [1] Bioconductor GenomicAlignments 1.29.0 2021-05-19 [1] Bioconductor GenomicRanges * 1.45.0 2021-05-19 [1] Bioconductor ggplot2 * 3.3.5 2021-06-25 [1] RSPM (R 4.1.0) glue 1.4.2 2020-08-27 [1] RSPM (R 4.1.0) gtable 0.3.0 2019-03-25 [1] RSPM (R 4.1.0) haven 2.4.1 2021-04-23 [1] RSPM (R 4.1.0) hms 1.1.0 2021-05-17 [1] RSPM (R 4.1.0) htmltools 0.5.1.1 2021-01-22 [1] RSPM (R 4.1.0) httr 1.4.2 2020-07-20 [1] RSPM (R 4.1.0) IRanges * 2.27.0 2021-05-19 [1] Bioconductor jsonlite 1.7.2 2020-12-09 [1] RSPM (R 4.1.0) knitr 1.33 2021-04-24 [1] RSPM (R 4.1.0) lattice 0.20-44 2021-05-02 [2] CRAN (R 4.1.0) lifecycle 1.0.0 2021-02-15 [1] RSPM (R 4.1.0) lubridate 1.7.10 2021-02-26 [1] RSPM (R 4.1.0) magrittr 2.0.1 2020-11-17 [1] RSPM (R 4.1.0) Matrix 1.3-4 2021-06-01 [1] RSPM (R 4.1.0) MatrixGenerics 1.5.2 2021-08-02 [1] Bioconductor matrixStats 0.60.0 2021-07-26 [1] RSPM (R 4.1.0) modelr 0.1.8 2020-05-19 [1] RSPM (R 4.1.0) munsell 0.5.0 2018-06-12 [1] RSPM (R 4.1.0) pillar 1.6.2 2021-07-29 [1] RSPM (R 4.1.0) pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.1.0) plyranges * 1.13.1 2021-06-28 [1] Bioconductor purrr * 0.3.4 2020-04-17 [1] RSPM (R 4.1.0) R6 2.5.0 2020-10-28 [1] RSPM (R 4.1.0) Rcpp 1.0.7 2021-07-07 [1] RSPM (R 4.1.0) RCurl 1.98-1.3 2021-03-16 [1] RSPM (R 4.1.0) readr * 2.0.0 2021-07-20 [1] RSPM (R 4.1.0) readxl 1.3.1 2019-03-13 [1] RSPM (R 4.1.0) reprex 2.0.0 2021-04-02 [1] RSPM (R 4.1.0) restfulr 0.0.13 2017-08-06 [1] RSPM (R 4.1.0) rjson 0.2.20 2018-06-08 [1] RSPM (R 4.1.0) rlang 0.4.11 2021-04-30 [1] RSPM (R 4.1.0) rmarkdown 2.9 2021-06-15 [1] RSPM (R 4.1.0) Rsamtools 2.9.1 2021-06-17 [1] Bioconductor rstudioapi 0.13 2020-11-12 [1] RSPM (R 4.1.0) rtracklayer 1.53.0 2021-05-19 [1] Bioconductor rvest 1.0.1 2021-07-26 [1] RSPM (R 4.1.0) S4Vectors * 0.31.0 2021-05-19 [1] Bioconductor scales 1.1.1 2020-05-11 [1] RSPM (R 4.1.0) sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.1.0) stringi 1.7.3 2021-07-16 [1] RSPM (R 4.1.0) stringr * 1.4.0 2019-02-10 [1] RSPM (R 4.1.0) SummarizedExperiment 1.23.1 2021-06-24 [1] Bioconductor tibble * 3.1.3 2021-07-23 [1] RSPM (R 4.1.0) tidyr * 1.1.3 2021-03-03 [1] RSPM (R 4.1.0) tidyselect 1.1.1 2021-04-30 [1] RSPM (R 4.1.0) tidyverse * 1.3.1 2021-04-15 [1] RSPM (R 4.1.0) tzdb 0.1.2 2021-07-20 [1] RSPM (R 4.1.0) utf8 1.2.2 2021-07-24 [1] RSPM (R 4.1.0) vctrs 0.3.8 2021-04-29 [1] RSPM (R 4.1.0) vroom * 1.5.3 2021-07-14 [1] RSPM (R 4.1.0) withr 2.4.2 2021-04-18 [1] RSPM (R 4.1.0) xfun 0.24 2021-06-15 [1] RSPM (R 4.1.0) XML 3.99-0.6 2021-03-16 [1] RSPM (R 4.1.0) xml2 1.3.2 2020-04-23 [1] RSPM (R 4.1.0) XVector 0.33.0 2021-05-19 [1] Bioconductor yaml 2.2.1 2020-02-01 [1] RSPM (R 4.1.0) zlibbioc 1.39.0 2021-05-19 [1] Bioconductor [1] /usr/local/lib/R/site-library [2] /usr/local/lib/R/library
The output of sessioninfo::session_info() includes relevant GitHub installation information and other details that are missed by sessionInfo().
sessioninfo::session_info()
sessionInfo()
Context
I try to use reduce_ranges on the example found in https://bioconductor.github.io/BiocWorkshops/fluent-genomic-data-analysis-with-plyranges.html but I get a strange output:
Code
R session information
The output of
sessioninfo::session_info()includes relevant GitHub installation information and other details that are missed bysessionInfo().