FourCseq- adding information manually
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tlgolan • 0
@tlgolan-10804
Last seen 5.0 years ago

Hi,

I am trying to manually add information (rowRanges and primer data) to my 'fc' object. This is my code (the relevant parts to my problem):

fragmented_Rn6=read.table(file="valid fragments only_Rn6.tab",header=TRUE) 
fragmented_Rn6$leftSize=as.numeric(fragmented_Rn6$leftSize)
fragmented_Rn6$rightSize =as.numeric(fragmented_Rn6$rightSize)
gr=makeGRangesFromDataFrame(fragmented_Rn6,keep.extra.columns=TRUE,ignore.strand=TRUE,seqnames.field="chr", start.field="start",end.field = "end",starts.in.df.are.0based=TRUE ) 
rowRanges(fc)=gr

colData(fc)$chr= factor("chr5")   #chr of the viewpoint; class- factor
colData(fc)$start= 164790443L     # start point of viewpoint fragment; class- integer
colData(fc)$end= 164793939L       # end point of viewpoint fragment; class- integer

 

When I use the getZscore function I keep getting this Error:

> minCount=40
> fcf = getZScores(fc, removeZeros = TRUE,minCount=minCount,fitFun =distFitMonotoneSymmetric)

Error in Ops.factor(runValue(e1)[which1], runValue(e2)[which2]) : 
  level sets of factors are different

Does anyone know why?

 

fourcseq • 457 views
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felix.klein ▴ 150
@felixklein-6900
Last seen 3.1 years ago
Germany
Hi Tal, check that you have the same factor levels. I would assume, that fragemented_Rn6 has all chromosomes as level while colData only has chr5. If you add the missing levels there it should work. Best regards, Felix
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