Question: ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds
0
gravatar for enricoferrero
3.4 years ago by
enricoferrero570
Switzerland
enricoferrero570 wrote:

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!

 

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by enricoferrero570
Answer: ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds
1
gravatar for enricoferrero
3.4 years ago by
enricoferrero570
Switzerland
enricoferrero570 wrote:

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))
ADD COMMENTlink written 3.4 years ago by enricoferrero570
Answer: ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds
0
gravatar for Guangchuang Yu
3.4 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:
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 COMMENTlink written 3.4 years ago by Guangchuang Yu1.1k
1

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 REPLYlink written 3.4 years ago by enricoferrero570
1

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 REPLYlink written 3.4 years ago by Guangchuang Yu1.1k
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