[BioC] ChIPpeakAnno makeVennDiagram problems

[Zhu, Lihua (Julie)]

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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