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Question: Questions about SomaticSignatures package
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gravatar for Asma rabe
3.0 years ago by
Asma rabe290
Japan
Asma rabe290 wrote:

Hi,

I would like to thank the authors of SomaticSignatures  for the helpful package and for support on bioconductor forum.

Although the vignette is clear, I suggest that you add an example on how to start from text file in this format:

Chr Stt end Ref Var SampleID study

This will be much more easy for many readers to start processing there own data

Data<-read.table("file.txt")

colnames(Data)<-c("Chr","Start","End","Ref","Var","Sample","study")

sca_vr = VRanges(seqnames=Data$Chr,ranges=IRanges(start=Data$Start,width=1),ref=Data$Ref,alt=Data$Var,study=Data$study)

…..

….

other steps are as exactly in vignette.

#=====================

In case of using fast to get mutation context, I could not find mutational context function

sca_vr = VRanges(seqnames=Data$Chr,ranges=IRanges(start=Data$Start,width=1),ref=Data$Ref,alt=Data$Var,study=Data$study)

fa_A = FastaFile("human_hg19.ucsc.fa")

vr_A = mutationalContext(sca_vr, fa_A)
Error: could not find function "mutationalContext"

When i tried mutationContext , i got this error

vr_A = mutationContext(sca_vr,fa_A)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘getSeq’ for signature ‘"FastaFile"’

Any idea??

#=====================

In mutational signatures plot y-axis represents the contribution of each motif in the signatures. How this contribution is estimated?

Thank you very much.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Asma rabe290

Hi Asma,

Have you figure out how to input your own data with VRanges?

I also faced with same problem. If you already success, please let me know.

 

Bests,

Shengfeng

 

 

ADD REPLYlink written 2.4 years ago by shengfeng0
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