Comments (3)
A quick update on the situation: based on the responses in the linked GitHub issue, I used the patched version of GenomeInfoDb and received a different set of errors+warnings.
Calling toGRanges()
produces no errors, but the following warning: cannot switch some of GRCm38's seqlevels from NCBI to UCSC style
. If this annotation data is used with annotatePeakInBatch()
, this warning appears: not all the seqnames of myPeakList is in the AnnotationData.The 2 combined objects have no sequence levels in common.
Lastly, attempting to add gene ID's and feature names to these peaks with addGeneIDs()
fails entirely, with the error Error: There is no feature column in annotatedPeak or annotatedPeak has size 0!
I hope this provides some useful context, thank you in advance for your help!
from chippeakanno.
Hi,
Thank you for reporting this. I patched the package to handle this error. Please try to update the package to development version and try it again. Let me know if you still have question.
Jianhong.
from chippeakanno.
Hi Jianhong,
Your patch worked great! Thank you so much for fixing it, you have saved a critical component of my analysis.
-Jared
from chippeakanno.
Related Issues (20)
- Error with `bindingType` in `annotatePeakInBatch` HOT 2
- Questions on the how genomicElementDistribution works HOT 1
- error in enrichmentPlot() when providing a partially empty GO object HOT 1
- toGRanges() can't read in file name HOT 1
- Differences between bedtools overlap / findOverlaps and findOverlapsOfPeaks HOT 10
- disjointExons removed in Bioconductor 3.17 HOT 1
- How to understand otherExon HOT 7
- `findOverlapsOfPeaks(gr1, gr2)` Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs. HOT 6
- How to set the circle size same proportion of the number of peaks when there are more than 2 sets using `makeVennDiagram`? HOT 5
- oligoSummary not populating the motif matrix output field HOT 2
- makeVennDiagram fails with error 'Unexpected parameter length for "col"' HOT 4
- cvglists rtracklayer import error: Error in stop_if_wrong_length(what, ans_len) 'ranges' must have the length of the object to construct HOT 4
- hello,I don't know how to deal with it,can you help me figure it out. thanks HOT 8
- makeVennDiagram produces undesired console output HOT 6
- Regarding oligoSummary() HOT 1
- opened in error
- anno gene in heatmap HOT 4
- Number of Overlap Peaks HOT 1
- makeVennDiagram HOT 4
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