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.
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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