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HenrikBengtsson / aroma.cn.eval

🔬 R package: aroma.cn.eval
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'findChangePoints' assumes sorted input data #1

Open pneuvial opened 9 years ago

pneuvial commented 9 years ago 
> cnR
SegmentedCopyNumbers:
Name: ROC
Number of rows: 28931
Number of columns: 4
Columns: chromosome [numeric], x [numeric], cn [numeric], state* [numeric]
RAM: 0.56MB
Chromosomes: 0 [1]
Number of loci: 28931
Position range: [1.00006e+07,2.19998e+07]
Mean distance between loci: 414.768
> table(getStates(cnR))

   -1     0 
 8378 15378 
> cps <- findChangePointsByState(cnR, na.rm=TRUE, ends=TRUE)
> cps
 [1] 10000564 17999681 15998628 17981854 15946940 18055980 15981472 18056784
 [9] 15976855 18006812 15990232 17986574 16039763 17999701 15997448 18055141
[17] 16066085 17984982 16049780 18028110 15995324 18000603 15994306 18052537
[25] 15999434 17994246 16015902 17999194 15982423 17192758 16001896 17998905
[33] 16005792 17985927 15989360 17974496 19027778 17986384 16000216 17998410
[41] 16004417 18024618 21999798
HenrikBengtsson commented 9 years ago

So

cnR <- sort(cnR)

sorts RawGenomicSignals objects along the genome (and SegmentedCopyNumbers inherits from that class). However, I'm not sure if it mess other things up. Worth trying though.