Problems using intansv...
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Phil Ross ▴ 10
@phil-ross-6503
Last seen 7.7 years ago
Hello, Within my lab we’ve recently started trying to incorporate different CNV detection programs into our pipeline and found the intansv (http://www.bioconductor.org/packages/2.13/bioc/html/intansv.html) package which is great for integrating the results of different CNV detection programs, combining them into one output dataset, and then using a GFF file to annotate the CNVs that were called by each. However, I’m consistently getting an error that states the following… Error in `$<-.data.frame`(`*tmp*`, "parent", value = c("PF3D7_0100100", : replacement has 6685 rows, data has 7245 The tool isn’t very complicated and I’m not sure why I consistently get this error no matter how I import the GFF file or which cnvcalls output file I use. Here is the code I’m currently using… ## LOAD LIBRARIES library(intansv) library(GenomicRanges) library(rtracklayer) ## IMPORT GFF FILE ### WARNING: PlasmoDB gff file comes improperly formatted...on first commented line change tab to space between 'gff-version' and '3' gffAnnotation <- import.gff("/Users/philross/Desktop/PlasmoDB-9.3_Pfalciparum3D7.gff", asRangedData=FALSE) ## IMPORT CNVNATOR CALLS ### WARNING: Make sure the file doesn't contain a header. If it does insert '#' as the first character on the first line structuralVariation <- readCnvnator(dataDir="/Users/philross/Desktop/cnvnator", method="CNVnator") ## SV ANNOTATION sa <- llply(structuralVariation, svAnnotation, genomeAnnotation=gffAnnotation) The error occurs while running the svAnnotation function seen on the last line. While trying to sort through the debugger I notice that the error occurs between this two calls within the svAnnotation function itself: structuralVariationGeneAnnoNna[structuralVariationGeneAnnoNna$anno tation != "gene", ]$parent <- (genomeAnnotation[as.numeric(structuralVar iationGeneAnnoNna[structuralVariationGeneAnnoNna$annotation != "gene", ]$subject)]$Parent)@unlistData structuralVariationGeneAnnoNa$parent <- NA So it’s the second line there that’s causing the error which I don’t understand…Any ideas? Am I not importing the gene annotation file correctly? Not using arguments somewhere where I should be? Perhaps it’s something wrong with the way the GFF file is formatted? Maintainer: "Wen Yao <ywhzau@gmail.com>” Any help would be greatly appreciated! Best, Phil Ross [[alternative HTML version deleted]]
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Hi Phill,

I am using intansv and am running into a similar problem.  I was wondering if you figured out how to get around it?

Thanks

Natalie

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akv22 • 0
@akv22-10921
Last seen 5.9 years ago

I have the same problem. Any solutions yet?

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