Hi all,
I wanted to change the default parameters of the glad algorithm. This does
not work:
glad <- GladModel(cesN, lambdabreak=20, param=c(d=20))
fit(glad, arrays=1, chromosomes=22, verbose=verbose)
[...]
20140214 21:18:11| Setting up GLAD data structure...done
20140214 21:18:11| User and segmentation arguments:
List of 2
$ lambdabreak: num 20
$ param : Named num 20
..- attr(*, "names")= chr "d"
20140214 21:18:11| Final arguments:
List of 2
$ :List of 1
..$ profileValues:'data.frame': 43799 obs. of 5 variables:
.. ..$ LogRatio : num [1:43799] 0.07282 -0.03324 0.07527 0.00626
0.09242 ...
.. ..$ PosOrder : int [1:43799] 1 2 3 4 5 6 7 8 9 10 ...
.. ..$ Chromosome : int [1:43799] 22 22 22 22 22 22 22 22 22 22 ...
.. ..$ PosBase : num [1:43799] 16052543 16052647 16060231
16061342 16066888 ...
.. ..$ ChromosomeChar: int [1:43799] 22 22 22 22 22 22 22 22 22 22 ...
..- attr(*, "class")= chr "profileCGH"
$ verbose: logi TRUE
20140214 21:18:11| Setting up method arguments...done
20140214 21:18:11| Looking for cached results...
20140214 21:18:11| Looking for cached results...done
20140214 21:18:11| Calling glad() of GLAD...
[...]
Although the paramaters appear in the log as optional arguments and I
removed the gladModel directory on my disk, I always get the same results
as with the default arguements. Running glad() manually works:
cn <- extractRawCopyNumbers(glad, array=1, chromosome=22)
data <- as.data.frame(cn)
colnames(data) <- c("Chromosome", "Position", "LogRatio")
data$PosOrder <- order(data$Position)
library("GLAD")
profile <- as.profileCGH(data)
res <- glad(profile, lambdabreak=20, param=c(d=20))
Over segmentation is much reduced. I wonder whether it is correct to pass
the arguments to the GladModel constructor. It seems to work according to
what I read in this forum.
Thanks and best regards,
Hans-Ulrich
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-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] GLAD_2.26.0 aroma.light_1.32.0 matrixStats_0.8.12
[4] aroma.affymetrix_2.11.1 aroma.core_2.11.0 R.devices_2.7.2
[7] R.filesets_2.3.0 R.utils_1.28.4 R.oo_1.15.8
[10] affxparser_1.34.0 R.methodsS3_1.5.2
loaded via a namespace (and not attached):
[1] aroma.apd_0.4.0 digest_0.6.4 DNAcopy_1.36.0 PSCBS_0.40.2
[5] R.cache_0.9.0 R.huge_0.6.0 R.rsp_0.9.28 tools_3.0.1
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