[BioC] ChIPpeakAnno makeVennDiagram problems
Zhu, Lihua (Julie)
Julie.Zhu at umassmed.edu
Tue May 28 21:54:06 CEST 2013
Vince,
Many thanks for the feedback and the great test examples! Jianhong has
resolved the issue. Please download the newest dev version (revision 76936)
and let us know if it works for you.
Best regards,
Julie
On 5/24/13 12:10 PM, "Vincent Schulz" <Vincent.Schulz at yale.edu> wrote:
> Hi Julie,
>
> The new version is better, but not quite there. I am still having troubles
> with a 4 way venn,
> possibly because of not all of the datasets having peaks on all chromosomes
> (eg Y), but this is just
> a guess. I get the same error
> Error in seq.default(cnt, length.out = counts[i]) :
> length must be non-negative number
>
> I could send you the data--it isn't tiny but isn't huge either. There is
> another problems that
> perhaps could be addressed first since it is more defined, see below.
>
> Thanks,
>
> Vince
>
>
>
> peaks1 = RangedData(IRanges(start = c(1, 100, 200),
> end = c(2, 101, 201), names = c("Site1", "Site2", "Site3")),
> space = c("1", "1", "1"),
> strand=as.integer(1),feature=c("a","b","f"))
> peaks2 = RangedData(IRanges(start = c(1, 100, 200),
> end = c(1, 101, 201), names = c("Site1", "Site2", "Site3")),
> space = c("2", "2", "2"),
> strand=as.integer(1),feature=c("a","b","f"))
> peaks3 = RangedData(IRanges(start = c(1, 100, 200),
> end = c(3, 103, 203), names = c("Site1", "Site2", "Site3")),
> space = c("1", "2", "2"),
> strand=as.integer(1),feature=c("a","b","f"))
> peaks4 = RangedData(IRanges(start = c(1, 100, 200),
> end = c(2, 101, 201), names = c("Site1", "Site2", "Site3")),
> space = c("1", "2", "2"),
> strand=as.integer(1),feature=c("a","b","f"))
> makeVennDiagram(RangedDataList(peaks1,peaks2,peaks3),
> NameOfPeaks=c("TF1", "TF2","TF3"),
> totalTest=100,scaled=F, euler.d=F)
> #Error in findOverlappingPeaks(findOverlappingPeaks(Peaks[[1]], Peaks[[2]], :
> # No valid Peaks1 passed in. It needs to be RangedData object
>
> #data same as above except first chrom of first range in peaks2
> peaks1 = RangedData(IRanges(start = c(1, 100, 200),
> end = c(2, 101, 201), names = c("Site1", "Site2", "Site3")),
> space = c("1", "1", "1"),
> strand=as.integer(1),feature=c("a","b","f"))
> peaks2 = RangedData(IRanges(start = c(1, 100, 200),
> end = c(1, 101, 201), names = c("Site1", "Site2", "Site3")),
> space = c("1", "2", "2"),
> strand=as.integer(1),feature=c("a","b","f")) #note first
> #chrom diff from above!
> peaks3 = RangedData(IRanges(start = c(1, 100, 200),
> end = c(3, 103, 203), names = c("Site1", "Site2", "Site3")),
> space = c("1", "2", "2"),
> strand=as.integer(1),feature=c("a","b","f"))
> peaks4 = RangedData(IRanges(start = c(1, 100, 200),
> end = c(2, 101, 201), names = c("Site1", "Site2", "Site3")),
> space = c("1", "2", "2"),
> strand=as.integer(1),feature=c("a","b","f"))
> makeVennDiagram(RangedDataList(peaks1,peaks2,peaks3),
> NameOfPeaks=c("TF1", "TF2","TF3"),
> totalTest=100,scaled=F, euler.d=F)
> #is fine, as is below
> makeVennDiagram(RangedDataList(peaks1,peaks2,peaks3,peaks4),
> NameOfPeaks=c("TF1", "TF2","TF3",
> "TF4"),
> totalTest=100,scaled=F, euler.d=F)
>
> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> 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=C 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 grid stats graphics grDevices utils datasets
> [8] methods base
>
> other attached packages:
> [1] RSvgDevice_0.6.4.2 ChIPpeakAnno_2.9.1
> [3] GenomicFeatures_1.13.8 limma_3.17.12
> [5] org.Hs.eg.db_2.9.0 GO.db_2.9.0
> [7] RSQLite_0.11.3 DBI_0.2-7
> [9] AnnotationDbi_1.23.11 BSgenome.Ecoli.NCBI.20080805_1.3.17
> [11] BSgenome_1.29.0 GenomicRanges_1.13.14
> [13] Biostrings_2.29.3 XVector_0.1.0
> [15] IRanges_1.19.8 multtest_2.17.0
> [17] Biobase_2.21.2 biomaRt_2.17.0
> [19] BiocGenerics_0.7.2 VennDiagram_1.6.0
> [21] Cairo_1.5-2
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-5 MASS_7.3-26 RCurl_1.95-4.1
> Rsamtools_1.13.15
> [5] rtracklayer_1.21.5 splines_3.0.1 stats4_3.0.1 survival_2.37-4
> [9] tcltk_3.0.1 tools_3.0.1 XML_3.96-1.1 zlibbioc_1.7.0
>
>
>
>
>
> On 5/22/2013 4:51 PM, Zhu, Lihua (Julie) wrote:
>> Vincent,
>>
>> It has been fixed in the dev version 2.9.1.
>>
>> Many thanks for the the feedback and the detailed examples!
>>
>> Best regards,
>>
>> Julie
>>
>>
>> On 5/22/13 1:47 PM, "Vincent Schulz" <Vincent.Schulz at yale.edu> wrote:
>>
>>> Hi,
>>>
>>> I am having problems with ChIPpeakAnno makeVennDiagram problems when the
>>> regions of interest do not
>>> overlap. This is coming up for me in comparing 4 datasets where two of the
>>> datasets don't overlap.
>>> It would be great if the function could properly output 0 in the
>>> non-overlapping segments.
>>>
>>> Thanks,
>>>
>>> Vince
>>>
>>>
>>> #toy example to show the issues
>>> library(ChIPpeakAnno)
>>>
>>>
>>> #this is OK
>>> peaks1 = RangedData(IRanges(start = c(1, 100, 200),
>>> end = c(2, 101, 201), names = c("Site1", "Site2", "Site3")),
>>> space = c("1", "1", "1"),
>>> strand=as.integer(1),feature=c("a","b","f"))
>>> peaks2 = RangedData(IRanges(start = c(1, 100, 200),
>>> end = c(2, 101, 201), names = c("Site1", "Site2", "Site3")),
>>> space = c("1", "1", "1"),
>>> strand=as.integer(1),feature=c("a","b","f"))
>>> makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1",
>>> "TF2"),
>>> totalTest=100,scaled=F, euler.d=F)
>>> #below gives error
>>> peaks1 = RangedData(IRanges(start = c(1, 100, 200),
>>> end = c(2, 101, 201), names = c("Site1", "Site2", "Site3")),
>>> space = c("1", "1", "1"),
>>> strand=as.integer(1),feature=c("a","b","f"))
>>> peaks2 = RangedData(IRanges(start = c(1, 100, 200),
>>> end = c(2, 101, 201), names = c("Site1", "Site2", "Site3")),
>>> space = c("2", "2", "2"),
>>> strand=as.integer(1),feature=c("a","b","f"))
>>> makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1",
>>> "TF2"),
>>> totalTest=100,scaled=F, euler.d=F)
>>> #Error in `colnames<-`(`*tmp*`, value = c("TF1", "chr", "TF2")) :
>>> # attempt to set 'colnames' on an object with less than two dimensions
>>> #below gives error (but it works in R2.15!)
>>> peaks1 = RangedData(IRanges(start = c(1, 100, 200),
>>> end = c(2, 101, 201), names = c("Site1", "Site2", "Site3")),
>>> space = c("1", "1", "1"),
>>> strand=as.integer(1),feature=c("a","b","f"))
>>> peaks2 = RangedData(IRanges(start = c(5, 105, 205),
>>> end = c(6, 106, 206), names = c("Site1", "Site2", "Site3")),
>>> space = c("1", "1", "1"),
>>> strand=as.integer(1),feature=c("a","b","f"))
>>> makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1",
>>> "TF2"),
>>> totalTest=100,scaled=F, euler.d=F)
>>> #Error in seq.default(cnt, length.out = counts[i]) :
>>> # length must be non-negative number
>>> #In addition: Warning messages:
>>> #1: In min(p1.inBoth, p2.inBoth) :
>>> # no non-missing arguments to min; returning Inf
>>> #2: In findVennCounts(Peaks = Peaks, NameOfPeaks = NameOfPeaks, maxgap =
>>> maxgap, :
>>> # negative counts generated when multiple peaks overlap with one peak!
>>> #
>>> sessionInfo()
>>> R version 3.0.1 (2013-05-16)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> 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=C 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 grid stats graphics grDevices utils datasets
>>> [8] methods base
>>>
>>> other attached packages:
>>> [1] RSvgDevice_0.6.4.2 Cairo_1.5-2
>>> [3] ChIPpeakAnno_2.8.0 GenomicFeatures_1.12.1
>>> [5] limma_3.16.4 org.Hs.eg.db_2.9.0
>>> [7] GO.db_2.9.0 RSQLite_0.11.3
>>> [9] DBI_0.2-7 AnnotationDbi_1.22.5
>>> [11] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.28.0
>>> [13] GenomicRanges_1.12.4 Biostrings_2.28.0
>>> [15] IRanges_1.18.1 multtest_2.16.0
>>> [17] Biobase_2.20.0 biomaRt_2.16.0
>>> [19] BiocGenerics_0.6.0 VennDiagram_1.6.0
>>> [21] BiocInstaller_1.10.1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] bitops_1.0-5 MASS_7.3-26 RCurl_1.95-4.1
>>> Rsamtools_1.12.3
>>> [5] rtracklayer_1.20.2 splines_3.0.1 stats4_3.0.1
>>> survival_2.37-4
>>> [9] tcltk_3.0.1 tools_3.0.1 XML_3.96-1.1
>>> zlibbioc_1.6.0
>>>
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