Question

ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds

0

Entering edit mode

enricoferrero ▴ 660

@enricoferrero-6037

Last seen 3.0 years ago

Switzerland

Hello,

I'm getting a subscript out of bound error when using plotvenn() from ChIPseeker on a list of GRanges objects:

# load libraries
library(GenomicRanges)
library(ChIPseeker)

# get some GRanges objects
example(GRanges)

# check intersection
intersect(some.gr, longGR)
GRanges object with 7 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1   [6, 10]      +
  [2]     chr1   [5, 10]      *
  [3]     chr2   [2, 10]      +
  [4]     chr2   [1, 10]      -
  [5]     chr2   [4, 10]      *
  [6]     chr3   [7, 10]      +
  [7]     chr3   [9, 10]      -
  -------
  seqinfo: 3 sequences from mock1 genome

# visualise intersection with Venn diagram
vennplot(list(some.gr, longGR))
Error in ss[[1]] : subscript out of bounds

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

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

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

other attached packages:
 [1] ChIPseeker_1.8.3     GenomicRanges_1.24.0 GenomeInfoDb_1.8.1   IRanges_2.6.1        S4Vectors_0.10.1     BiocGenerics_0.18.0
 [7] nvimcom_0.9-16       BiocInstaller_1.22.3 colorout_1.0-2       setwidth_1.0-4

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5                             RColorBrewer_1.1-2                      plyr_1.8.4
 [4] XVector_0.12.0                          GenomicFeatures_1.24.2                  bitops_1.0-6
 [7] tools_3.3.0                             zlibbioc_1.18.0                         boot_1.3-18
[10] biomaRt_2.28.0                          gridBase_0.4-7                          RSQLite_1.0.0
[13] gtable_0.2.0                            TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 DBI_0.4-1
[16] gridExtra_2.2.1                         UpSetR_1.2.0                            rtracklayer_1.32.0
[19] dplyr_0.4.3                             caTools_1.17.1                          gtools_3.5.0
[22] Biostrings_2.40.1                       grid_3.3.0                              Biobase_2.32.0
[25] R6_2.1.2                                plotrix_3.6-2                           AnnotationDbi_1.34.3
[28] XML_3.98-1.4                            BiocParallel_1.6.2                      gdata_2.17.0
[31] magrittr_1.5                            ggplot2_2.1.0                           gplots_3.0.1
[34] Rsamtools_1.24.0                        scales_0.4.0                            GenomicAlignments_1.8.0
[37] assertthat_0.1                          SummarizedExperiment_1.2.2              colorspace_1.2-6
[40] KernSmooth_2.23-15                      RCurl_1.95-4.8                          munsell_0.4.3

Am I doing something wrong?

Thank you!

chipseeker venn vennplot genomicranges granges • 2.3k views

ADD COMMENT • link 8.4 years ago enricoferrero ▴ 660

0

Entering edit mode

Guangchuang Yu ★ 1.2k

@guangchuang-yu-5419

Last seen 18 days ago

China/Guangzhou/Southern Medical Univer…

pls checkout the vignette, https://www.bioconductor.org/packages/3.3/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html#overlap-of-peaks-and-annotated-genes On Mon, Jul 4, 2016 at 4:25 PM, enricoferrero [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User enricoferrero <https: support.bioconductor.org="" u="" 6037=""/> wrote Question: > ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds > <https: support.bioconductor.org="" p="" 84607=""/>: > > Hello, > > I'm getting a subscript out of bound error when using plotvenn() from ChIPseeker > on a list of GRanges objects: > > # load libraries > library(GenomicRanges) > library(ChIPseeker) > > # get some GRanges objects > example(GRanges) > > # check intersection > intersectsome.gr, longGR) > > GRanges object with 7 ranges and 0 metadata columns: > seqnames ranges strand > <rle> <iranges> <rle> > [1] chr1 [6, 10] + > [2] chr1 [5, 10] * > [3] chr2 [2, 10] + > [4] chr2 [1, 10] - > [5] chr2 [4, 10] * > [6] chr3 [7, 10] + > [7] chr3 [9, 10] - > ------- > seqinfo: 3 sequences from mock1 genome# visualise intersection with Venn diagram > > vennplotlistsome.gr, longGR)) > > Error in ss[[1]] : subscript out of bounds > > > sessionInfo() > R version 3.3.0 (2016-05-03) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=C > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=C LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ChIPseeker_1.8.3 GenomicRanges_1.24.0 GenomeInfoDb_1.8.1 IRanges_2.6.1 S4Vectors_0.10.1 BiocGenerics_0.18.0 > [7] nvimcom_0.9-16 BiocInstaller_1.22.3 colorout_1.0-2 setwidth_1.0-4 > > loaded via a namespace (and not attached): > [1] Rcpp_0.12.5 RColorBrewer_1.1-2 plyr_1.8.4 > [4] XVector_0.12.0 GenomicFeatures_1.24.2 bitops_1.0-6 > [7] tools_3.3.0 zlibbioc_1.18.0 boot_1.3-18 > [10] biomaRt_2.28.0 gridBase_0.4-7 RSQLite_1.0.0 > [13] gtable_0.2.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 DBI_0.4-1 > [16] gridExtra_2.2.1 UpSetR_1.2.0 rtracklayer_1.32.0 > [19] dplyr_0.4.3 caTools_1.17.1 gtools_3.5.0 > [22] Biostrings_2.40.1 grid_3.3.0 Biobase_2.32.0 > [25] R6_2.1.2 plotrix_3.6-2 AnnotationDbi_1.34.3 > [28] XML_3.98-1.4 BiocParallel_1.6.2 gdata_2.17.0 > [31] magrittr_1.5 ggplot2_2.1.0 gplots_3.0.1 > [34] Rsamtools_1.24.0 scales_0.4.0 GenomicAlignments_1.8.0 > [37] assertthat_0.1 SummarizedExperiment_1.2.2 colorspace_1.2-6 > [40] KernSmooth_2.23-15 RCurl_1.95-4.8 munsell_0.4.3 > > Am I doing anything wrong? > > Thank you! > > > > ------------------------------ > > Post tags: chipseeker, venn, vennplot, genomicranges, granges > > You may reply via email or visit ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds > -- --~--~---------~--~----~------------~-------~--~----~ Guangchuang Yu, PhD Candidate State Key Laboratory of Emerging Infectious Diseases School of Public Health The University of Hong Kong Hong Kong SAR, China www: https://guangchuangyu.github.io -~----------~----~----~----~------~----~------~--~---

ADD COMMENT • link 8.4 years ago Guangchuang Yu ★ 1.2k

1

Entering edit mode

Thanks, however that doesn't really help because the example in the vignette is a list of gene IDs while here I'm using a list of GRanges.

The issue is that the list of GRanges has to be named (see my own answer). It might be worth adding it to the documentation.

ADD REPLY • link 8.4 years ago enricoferrero ▴ 660

1

Entering edit mode

thanks for your feedback. I have updated the code to throw error of 'input object should be a named list' if it is not.

ADD REPLY • link 8.4 years ago Guangchuang Yu ★ 1.2k

score 1 · Accepted Answer · 2016-07-04

I figured it out: vennplot() expects a named list.

This works:

# load libraries
library(GenomicRanges)
library(ChIPseeker)

# get some GRanges objects
example(GRanges)

# check intersection
intersect(some.gr, longGR)
GRanges object with 7 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1   [6, 10]      +
  [2]     chr1   [5, 10]      *
  [3]     chr2   [2, 10]      +
  [4]     chr2   [1, 10]      -
  [5]     chr2   [4, 10]      *
  [6]     chr3   [7, 10]      +
  [7]     chr3   [9, 10]      -
  -------
  seqinfo: 3 sequences from mock1 genome

# visualise intersection with Venn diagram
vennplot(list(gr1=some.gr, gr2=longGR))