[BioC] copyCountSegments(fit) failed exomeCopy

[Dan Spiegelman]

[key lines from earlier threads:]

love <love at ...> writes:
> This appears to be a bug for fitted objects which have no predicted
> variants (as the show command gives "percent normal state: 100%").  I will
> fix it.  

> > From: John linux-user <johnlinuxuser <at> yahoo.com>
> > Sent: Sunday, March 18, 2012 1:54 PM
> >> fit <- exomeCopy(exomecounts["chr1"],sample.name="HGPIPE_6159",
> > +                    X.names=c("bg","GC","GC.sq","width"),S=0:6,d=2)
> >>   show(fit)
> > 
> > ExomeCopy object
> > type: exomeCopy
> > percent normal state: 100%
> >> copyCountSegments(fit)
> > Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE =
> "IRanges")
> > : 
> >   solving row 1: negative widths are not allowed



Hello,

I am encountering a similar problem, though my data DOES have variants (i.e. is 
not 100% normal state). 

In setting up this analysis, I followed the procedure laid out in 
http://www.bioconductor.org/packages/2.9/bioc/vignettes/exomeCopy/inst/doc/exome
Copy.pdf virtually to the letter (except where my sample names and bamfile paths 
are concerned).

here the key lines of R code and output:
> fit <- 
exomeCopy(rdata["22"],sample.name="S12993",X.names=c("bg","GC","GC.sq","width"),
S=0:6,d=2)
> show(fit)
>  copyCountSegments(fit)
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
  solving row 113: negative widths are not allowed

here is the problematic line of my object, with 1 flanking row on both sides:
> rdata["22"][112:114,]
RangedData with 3 rows and 7 value columns across 1 space
     space               ranges |         bg        GC      GC.sq     width
  <factor>            <IRanges> |  <numeric> <numeric>  <numeric> <integer>
1       22 [17265302, 17265408] | 0.05448944 0.2803738 0.07860949       107
2       22 [17265409, 17265516] | 0.00000000 0.2685185 0.07210219       108
3       22 [17264572, 17264679] | 0.05448944 0.3981481 0.15852195       108
     S12993    S13514    S13045
  <integer> <integer> <integer>
1         0         8         2
2         0         1         0
3         0        31         2

as you can see above, the width in question is clearly not negative (value=108). 

I chose to show chr22 as an example, but in fact this problem appears in any 
other contig I use. 

Another strange issue is that my output for the show(fit) command is not simply 
the 3 lines I expected, but also includes the entire object (or as many lines as 
can be output to screen) plus a list of what look like debugging details 
(various variables with their associated values). This may or may not be germane 
to the problem. I am relatively new to R, and certainly have never used the 
IRanges package before. Maybe I'm missing something essential here (very 
likely). 


For reference purposes, here is a sample of the strange show(fit) output:
> show(fit)
...
[75841]  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00
[75846]  0.000000e+00  0.000000e+00  0.000000e+00  9.017138e+00  3.646900e+00
[75851]  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00
[75856]  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00
[75861]  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00
[75866]  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00
[75871]  0.000000e+00  0.000000e+00  0.000000e+00  5.866668e+00  3.430158e+00
[75876]  4.921296e-01  4.921296e-01  4.921296e-01  4.921296e-01  4.921296e-01
...
Slot "fx.par":
$S
[1] 0 1 2 3 4 5 6

$d
[1] 2

$normal.state
[1] 3

$fit.var
[1] FALSE


Slot "init.par":
$goto.cnv
[1] 1e-04

$goto.normal
[1] 0.05

$beta.hat
 intercept         bg         GC      GC.sq      width
30.5079982 60.4831813 -9.5804591  8.0219697  0.3726371

$phi.hat
[1] 0.1323678


Slot "final.par":
$goto.cnv

0.008851164

$goto.normal

0.2046247

$beta
 intercept         bg         GC      GC.sq      width
29.4767639 58.9864999 -2.0047419  1.7713904  0.1083148

$gamma
NULL

$phi
[1] 0.02133286


Slot "counts":
function gradient
     307       NA

Slot "convergence":
[1] 0

Slot "nll":
[1] 184461.1



finally, here are my session details:
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] exomeCopy_1.2.0     Rsamtools_1.8.4     Biostrings_2.24.1
[4] GenomicRanges_1.8.3 IRanges_1.14.2      BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] bitops_1.0-4.1 stats4_2.15.0  zlibbioc_1.2.0


Thank you for any help you can provide

Dan