On Fri, Feb 21, 2014 at 3:43 AM, Hans-Ulrich
<hans-ulrich.kl...@uni-muenster.de> wrote:
> Hi,
>
> I went through the code today and removed two lines from the function
> segmentByGLAD() from the arome.core package (version 2.11.0):
> # Cleaning out unknown parameters
> # keep <- (names(params) %in% names(formals));
> # params <- params[keep];
>
> After commenting out these two lines, the parameters appear in the logs
> under section "All parameters" (see below) and are passed to the glad()
> function.
Yes, thanks for reporting one this - it turns out that it has been the
behavior of GladModel for several years. I'm slowly pushing out the
next release of the Aroma Framework and a similar fix to yours will be
part of aroma.core 2.12.0. Packages can only be submitted one by one
to CRAN (and basically only one per day) so it'll still take a few
more days before you'll see it.
Cheers,
Henrik
>
> Best,
> Hans
>
>
> 20140221 12:27:10| Calling model fit function...
> 20140221 12:27:10| Optional arguments (may be ignored/may give an
> error/warning):
>
> List of 2
> $ lambdabreak: num 20
> $ param : Named num 20
> ..- attr(*, "names")= chr "d"
> 20140221 12:27:10| All arguments:
> List of 3
> $ :Classes 'RawCopyNumbers', 'RawGenomicSignals',
> 'RichDataFrame' and 'data.frame': 231306 obs. of 3 variables:
> ..$ chromosome: int [1:231306] 1 1 1 1 1 1 1 1 1 1 ...
> ..$ x : num [1:231306] 15266 48181 60839 61735 61808 ...
> ..$ cn : num [1:231306] -0.097 0.206 0.368 0.507 0.331 ...
> ..- attr(*, ".virtuals")= list()
> ..- attr(*, ".columnNamesTranslator")=function (names, invert = FALSE,
> ...)
> ..- attr(*, ".yLogBase")= num 2
>
> $ lambdabreak: num 20
> $ param : Named num 20
> ..- attr(*, "names")= chr "d"
> 20140221 12:27:10| Segmenting...
>
> Am Freitag, 14. Februar 2014 21:51:01 UTC+1 schrieb Hans-Ulrich:
>>
>> 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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