Hi Henrik,
That works, but with another sample, trying the last step suggested in the
vignette I get another error:
> fit <- callLOH(fit, verbose = -10)
> deltaCN <- estimateDeltaCN(fit, scale=1)
> fit <- callNTCN(fit, delta=deltaCN, verbose=-10)
..........
Identifying segments that are copy neutral states...done
Number of copy-neutral AB segments: 2
Extracting all copy neutral AB segments across all chromosomes into
one big segment...
chromosome tcnId dhId start end tcnNbrOfLoci tcnMean
tcnNbrOfSNPs
128 4 21 1 70750718 70913014 83 1.4003
38
488 18 9 1 4105338 7613644 2635 1.5945
1546
tcnNbrOfHets dhNbrOfLoci dhMean c1Mean c2Mean rohCall
abCall lohCall
128 16 16 0.1261 0.6118611 0.7884389 FALSE
TRUE NA
488 401 401 0.1307 0.6930494 0.9014506 FALSE
TRUE NA
Extracting all copy neutral AB segments across all chromosomes into
one big segment...done
Error: nbrOfSegments(fitNTCN) == 1 is not TRUE
Identifying copy neutral AB segments...done
calcStatsForCopyNeutralABs...done
Estimating TCN confidence interval of copy-neutral AB segments...done
Calling copy-neutral segments...done
callCopyNeutralByTCNofAB...done
By the way, I also tried
avgDH="median"
but I got this error
Error in bootstrapTCNandDHByRegion.PairedPSCBS(fit, statsFcn = statsFcn, :
INTERNAL ERROR: Incorrect DH mean!
Thanks,
Oscar
Oscar M. Rueda, PhD.
Postdoctoral Research Fellow, Caldas Lab, Breast Cancer Functional
Genomics.
University of Cambridge. Cancer Research UK Cambridge Institute.
Li Ka Shing Centre, Robinson Way.
Cambridge CB2 0RE
England
Please note that my email address will be changing to:
oscar.ru...@cruk.cam.ac.uk
>
>
>
>
>
>
>Henrik Bengtsson <henrik.bengts...@aroma-project.org>
> Feb 09 01:45PM -0800
>
>
>
>
>Hi Oscar,
>
>
>
>
>
>so you spotted a bug in the bootstrapping of the TCN mean-level
>
>
>estimates. It only affected segments that had been called to be in
>
>
>run-of-homozygosity (ROH) resulting in sampling from not all available
>
>
>TCN loci. The effect was incorrect TCN mean quantile estimates for
>
>
>those segments. For reasonable large segments this didn't matter
>
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>much, but for tiny segments (say < 5 loci) it made a small difference.
>
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>In your case the internal sanity checks caught this error in an ROH
>
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>segment of two loci.
>
>
>
>
>
>The bug has been fixed in PSCBS v0.32.5. You can grab it as usual:
>
>
>
>
>
>source("
>http://aroma-project.org/hbLite.R
>");
>
>
>hbInstall("PSCBS");
>
>
>
>
>
>I've verified that it now works with the sample data you've sent me.
>
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>Let me know if it solves it for all 126-60=66 samples where you had
>
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>problems.
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>
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>BTW, It is experimental/still early days, but you may want to move to
>
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>calculate DH using the median estimator instead of the default sample
>
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>mean. For more details, see 'Less biased Decrease of Heterozygosity
>
>
>(DH) estimates' in Section 'Experimental' of the 'Paired PSCBS'
>
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>vignette of PSCBS v0.32.5. Also, if you have saved 'fit' objects, you
>
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>don't have to rerun the segmentation (=finding the change points) to
>
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>achieve this; you can do fit <- updateMeans(fit, avgDH="median") and
>
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>then redo the calling.
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>Thanks for reporting.
>
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>
>
>
>Henrik
>
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>
>
>
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