Entering edit mode
Dan Spiegelman
▴
10
@dan-spiegelman-5248
Last seen 10.2 years ago
[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
