[BUG] Unexpected result reduce_ranges #92
Description
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
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 seqlengthsR session information
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/libraryThe output of sessioninfo::session_info() includes relevant GitHub installation information and other details that are missed by sessionInfo().