Hello,

I'm new here so I will introduce myself briefly. I'm working on NGS in
Lille (France) with data from a Solid and data from a GS Junior.
I have some data (from the GS Junior, processed with AVA) that I would like
to analyze with the R453Plus1 Toolbox.
So I ran the AVASet command. But I get an error :
"
Reading sample data ... done
Reading reference sequences ... done
Reading variant data ... Erreur dans end[deletions] =
as.numeric(variantSeq[deletions]) :
  NAs interdits dans les affectations indicées
"
(In english : Error in end[deletions] = as.numeric(variantSeq[deletions]) :
NAs forbidden in indexed affectations)

I have tested it on the example provided (extdata), and it worked well. But
when I look in the currentVariantDefs.txt file, there is no deletion ...
and the problem seems to be linked to the deletions.
The part of the code which give the error is to be in the readVariants
function.
"

# read position and sequence information for each variant
        num_variants=length(variantDefs$CVariant)
        referenceSeq=matrix(0, num_variants, 1)
        v_splits=strsplit(variantDefs$canonicalPattern, split="[\\)\\(,-]!?")
        variantSeq=sapply(v_splits, function(x)x[3])
        deletions=sapply(v_splits, function(x) x[1] == "d")
        start=as.numeric(sapply(v_splits,function(x)x[2]))
        end=start
        end[deletions]=as.numeric(variantSeq[deletions])
        del_length=end[deletions] - start[deletions] + 1
        del_length=sapply(del_length, function(x) paste(rep("-",x),
collapse=""))
"

Does anyone have had the same problem? Any idea to fix it?
Thanks by advance,


Olivia Jardin-Mathé
Plate-forme de Génomique Fonctionnelle et Structurale
Université Droit et Santé de Lille
IFR-114
Institut Pour la Recherche sur le Cancer de Lille
Place de Verdun
59045 LILLE cedex, FRANCE

	[[alternative HTML version deleted]]

