Question

FourCseq- adding information manually

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tlgolan • 0

@tlgolan-10804

Last seen 7.7 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 • 892 views

ADD COMMENT • link updated 7.8 years ago by felix.klein ▴ 150 • written 7.8 years ago by tlgolan • 0

score 1 · Answer 1 · 2016-07-10

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Entering edit mode

felix.klein ▴ 150

@felixklein-6900

Last seen 5.8 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

ADD COMMENT • link 7.8 years ago felix.klein ▴ 150