Question

GRanges nearest fails for non-overlapping regions

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dondelelcaro ▴ 10

@dondelelcaro-11528

Last seen 7.5 years ago

USA/Champaign/University of Illinois

GenomicRanges::nearest fails because strand(subject) != "-" is not logical:

>nearest(GRanges(seqnames=Rle("1",1),ranges=IRanges(start=1,end=10)),GRanges(seqnames=Rle("1",1),ranges=IRanges(start=100,end=120))) Error in base::which(x, arr.ind, useNames, ...) : argument to 'which' is not logical

Changing which(strand(subject)!="-") to which(as.logical(strand(subject)!="-"))

should fix this.

bug genomicranges granges nearest • 1.3k views

ADD COMMENT • link 7.5 years ago dondelelcaro ▴ 10

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sessionInfo? I am not able to reproduce this. Probably a namespace/generic issue, because there should be no need to coerce the logical Rle to a logical vector just to call which().

ADD REPLY • link 7.5 years ago Michael Lawrence ★ 11k

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R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] MASS_7.3-45                            
 [2] data.table_1.9.6                       
 [3] ggbio_1.22.0                           
 [4] ggplot2_2.0.0                          
 [5] Homo.sapiens_1.3.1                     
 [6] TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2
 [7] org.Hs.eg.db_3.1.2                     
 [8] GO.db_3.1.2                            
 [9] OrganismDbi_1.16.0                     
[10] GenomicFeatures_1.24.5                 
[11] GenomicRanges_1.26.1                   
[12] GenomeInfoDb_1.6.0                     
[13] AnnotationDbi_1.34.4                   
[14] IRanges_2.8.0                          
[15] S4Vectors_0.12.0                       
[16] Biobase_2.30.0                         
[17] BiocGenerics_0.20.0                    

loaded via a namespace (and not attached):
 [1] httr_0.6.1                    AnnotationHub_2.6.0          
 [3] splines_3.3.2                 Formula_1.2-1                
 [5] shiny_0.13.2                  interactiveDisplayBase_1.12.0
 [7] latticeExtra_0.6-26           RBGL_1.44.0                  
 [9] BSgenome_1.38.0               Rsamtools_1.22.0             
[11] RSQLite_1.0.0                 lattice_0.20-33              
[13] biovizBase_1.20.0             chron_2.3-47                 
[15] digest_0.6.8                  RColorBrewer_1.1-2           
[17] XVector_0.12.1                colorspace_1.2-6             
[19] htmltools_0.3.5               httpuv_1.3.3                 
[21] plyr_1.8.3                    XML_3.98-1.3                 
[23] biomaRt_2.26.1                zlibbioc_1.14.0              
[25] xtable_1.8-2                  scales_0.3.0                 
[27] BiocParallel_1.4.0            SummarizedExperiment_1.2.3   
[29] nnet_7.3-11                   hexbin_1.27.0                
[31] survival_2.38-3               magrittr_1.5                 
[33] mime_0.3                      GGally_0.5.0                 
[35] foreign_0.8-66                graph_1.50.0                 
[37] BiocInstaller_1.20.0          tools_3.3.2                  
[39] stringr_1.0.0                 munsell_0.4.2                
[41] cluster_2.0.3                 ensembldb_1.6.0              
[43] lambda.r_1.1.7                Biostrings_2.40.2            
[45] compiler_3.3.2                futile.logger_1.4.1          
[47] grid_3.3.2                    RCurl_1.95-4.7               
[49] dichromat_2.0-0               VariantAnnotation_1.16.3     
[51] bitops_1.0-6                  labeling_0.3                 
[53] gtable_0.1.2                  DBI_0.3.1                    
[55] reshape_0.8.5                 reshape2_1.4.1               
[57] R6_2.1.0                      GenomicAlignments_1.10.0     
[59] gridExtra_2.0.0               rtracklayer_1.32.2           
[61] Hmisc_3.17-1                  futile.options_1.0.0         
[63] stringi_1.0-1                 Rcpp_0.12.2                  
[65] rpart_4.1-10                  acepack_1.3-3.3

ADD REPLY • link 7.5 years ago dondelelcaro ▴ 10

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Looks like I can reduce this to:

> library("S4Vectors")
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
    Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums

> which(Rle(c("+","-"),c(5,3))=="-")
Error in base::which(x, arr.ind, useNames, ...) :
  argument to 'which' is not logical

ADD REPLY • link 7.5 years ago dondelelcaro ▴ 10

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Hmm. I've tried to replicate your environment but I still can't reproduce it. Maybe try removing and reinstalling Bioconductor from scratch? Something might be cached somewhere.

ADD REPLY • link 7.5 years ago Michael Lawrence ★ 11k

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OK, I'm still not sure what is causing this, but rebuilding S4Vectors and BiocGenerics fixes the issue.

The difference that I can tell is:

> which(Rle(c(TRUE,FALSE),c(5,3)))
Error in base::which(x, arr.ind, useNames, ...) :
  argument to 'which' is not logical
> showMethods("which")
Function: which (package BiocGenerics)
x="ANY"
x="Rle"
    (inherited from: x="ANY")

vs on a rebuild:

> which(Rle(c(TRUE,FALSE),c(5,3)))
[1] 1 2 3 4 5
> showMethods("which")
Function: which (package BiocGenerics)
x="ANY"
x="Rle"

Maybe it's because something changed in the S4 inheritance between R versions? Kind of out of my depth here.

ADD REPLY • link 7.5 years ago dondelelcaro ▴ 10