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$annotation !=  
        "gene", ]$parent <- (genomeAnnotation[as.numeric(structuralVariationGeneAnnoNna[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


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