Hi, I'd suggest that you use the Paired PSCBS segmentation method and the LOH caller proposed in the PSCBS paper:
A.B. Olshen*, H. Bengtsson*, P. Neuvial, P. Spellman, R.A. Olshen, V.E. Seshan, Parent-specific copy number in paired tumor-normal studies using circular binary segmentation, Bioinformatics, 2011. http://aroma-project.org/publications/ There is no high-level pipeline for doing this in the Aroma framework. We hope to get one up some day, but in the meanwhile, you can use the PSCBS package directly as suggested in vignette 'Paired parent-specific copy-number segmentation (Paired PSCBS) (low-level API after AS-CRMAv2)': http://aroma-project.org/vignettes/PairedPSCBS-lowlevel To call LOH after the segmentation step, just call callLOH(), but you first also need to call allelic-balance (AB) via callAB(), so do something like: fit <- segmentByPairedPSCBS(df, verbose=verbose); fit <- callAB(fit, verbose=verbose); fit <- callLOH(fit, verbose=verbose); and the columns 'abCall' and 'lohCall' (and a few others) will be added to the table of segments. BTW, by default Paired PSCBS will do TumorBoost for you (see above article), so you don't have to do it explicitly. However, since you've already done it, you can let segmentByPairedPSCBS() know by setting argument 'tbn=FALSE'. However however, the above vignette doesn't show how to extract the genotype calls nor the TumorBoost-normalized BAFs, so it is probably just easier to start with the signals before TumorBoost. Hope this helps Henrik On Wed, Nov 16, 2011 at 6:29 PM, sigrid <sigrid.ro...@gmail.com> wrote: > Hi, > I have successfully run TumorBoost on my samples. I would like to > retrieve the LOH calls from this. How should I proceed? > > > Here is the object I created: >> dsListf > $normal > AromaUnitFracBCnBinarySet: > Name: OvarianCancer > Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY > Full name: OvarianCancer,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY > Number of files: 1 > Names: 0800098 [1] > Path (to the first file): totalAndFracBData/OvarianCancer,ACC,ra,- > XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6 > Total file size: 7.18 MB > RAM: 0.00MB > > $tumor > AromaUnitFracBCnBinarySet: > Name: OvarianCancer > Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY > Full name: OvarianCancer,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY > Number of files: 1 > Names: 0800098 [1] > Path (to the first file): totalAndFracBData/OvarianCancer,ACC,ra,- > XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6 > Total file size: 7.18 MB > RAM: 0.00MB > > $tumorN > AromaUnitFracBCnBinarySet: > Name: OvarianCancer > Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,ACC,ra,-XY,BPN,-XY,AVG,FLN,- > XY,NGC > Full name: OvarianCancer,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,ACC,ra,- > XY,BPN,-XY,AVG,FLN,-XY,NGC > Number of files: 1 > Names: 0800098 [1] > Path (to the first file): totalAndFracBData/OvarianCancer,ACC,ra,- > XY,BPN,-XY,AVG,FLN,-XY,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,NGC/ > GenomeWideSNP_6 > Total file size: 7.18 MB > RAM: 0.00MB > > $callsN > AromaUnitGenotypeCallSet: > Name: OvarianCancer > Tags: ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,NGC > Full name: OvarianCancer,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY,NGC > Number of files: 1 > Names: 0800098 [1] > Path (to the first file): callData/OvarianCancer,ACC,ra,-XY,BPN,- > XY,AVG,FLN,-XY,NGC/GenomeWideSNP_6 > Total file size: 3.59 MB > RAM: 0.00MB > > Thank you! > > Regards, > > Sigrid > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
