IRanges constructor with FactorLists
Closed this issue · 3 comments
sa-lee commented
Hi @hpages,
I have a test failure for my package plyranges on the dev branch based on what I think is changes to IRanges, I'm not sure how to proceed so any ideas would be really helpful. Basically, I have some helpers of constructing Ranges from DFrames, and test case includes a column that has a FactorList. I've made a reprex of the problem below using the current dev version of IRanges:
suppressPackageStartupMessages(library(IRanges))
start <- 1:3
width <- 2:4
grps <- FactorList("a", c("b", "c"), "d")
grps
#> FactorList of length 3
#> [[1]] a
#> [[2]] b c
#> [[3]] d
# iranges constructor adding mcols
ir <- IRanges(start, width, grps = grps)
ir
#> IRanges object with 3 ranges and 1 metadata column:
#> start end width | grps
#> <integer> <integer> <integer> | <FactorList>
#> [1] 1 2 2 |
#> [2] 2 3 2 |
#> [3] 3 4 2 |
mcols(ir)$grps
#> FactorList of length 3
#> Error in RangeNSBS(x, start = start, end = end, width = width): the specified range is out-of-bounds
# iranges constructor without mcols
ir <- IRanges(start, width)
mcols(ir)[["grps"]] <- grps
ir
#> IRanges object with 3 ranges and 1 metadata column:
#> start end width | grps
#> <integer> <integer> <integer> | <FactorList>
#> [1] 1 2 2 |
#> [2] 2 3 2 |
#> [3] 3 4 2 |
mcols(ir)$grps
#> FactorList of length 3
#> Error in RangeNSBS(x, start = start, end = end, width = width): the specified range is out-of-boundsCreated on 2021-05-03 by the reprex package (v2.0.0)
Session info
sessioninfo::session_info()
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#> date 2021-05-03
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#> highr 0.9 2021-04-16 [1]
#> htmltools 0.5.1.1 2021-01-22 [1]
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#> Github (Bioconductor/IRanges@a5258ca)
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#> [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/librarysa-lee commented
It seems to be something to do with compression?
suppressPackageStartupMessages(library(IRanges))
start <- 1:3
width <- 2:4
grps <- FactorList("a", c("b", "c"), "d", compress = FALSE)
grps
#> FactorList of length 3
#> [[1]] a
#> [[2]] b c
#> [[3]] d
# iranges constructor adding mcols
ir <- IRanges(start, width, grps = grps)
ir
#> IRanges object with 3 ranges and 1 metadata column:
#> start end width | grps
#> <integer> <integer> <integer> | <FactorList>
#> [1] 1 2 2 | a
#> [2] 2 3 2 | b,c
#> [3] 3 4 2 | d
mcols(ir)$grps
#> FactorList of length 3
#> [[1]] a
#> [[2]] b c
#> [[3]] d
# iranges constructor without mcols
ir <- IRanges(start, width)
mcols(ir)[["grps"]] <- grps
ir
#> IRanges object with 3 ranges and 1 metadata column:
#> start end width | grps
#> <integer> <integer> <integer> | <FactorList>
#> [1] 1 2 2 | a
#> [2] 2 3 2 | b,c
#> [3] 3 4 2 | d
mcols(ir)$grps
#> FactorList of length 3
#> [[1]] a
#> [[2]] b c
#> [[3]] dCreated on 2021-05-03 by the reprex package (v2.0.0)