Hi,
I didn't get around to fix that in aroma.* v2.4.0. The only thing I
can say now is to "hack" (read update) the GLAD package and update its
cytoband data. For instance, you can load that data by:
> pathname <- system.file("data/cytoband.RData", package="GLAD");
> keys <- load(pathname);
> keys
[1] "cytoband"
> str(cytoband)
'data.frame': 395 obs. of 7 variables:
$ Chromosome: chr "1" "1" "1" "1" ...
$ Band : chr "p36.3" "p36.2" "p36.1" "p35" ...
$ Start : int 0 7100000 15600000 27700000 34300000 39800000 43800000 46500
000 50400000 60100000 ...
$ End : int 7100000 15600000 27700000 34300000 39800000 43800000 4650000
0 50400000 60100000 84600000 ...
$ Centro : num 0 0 0 0 0 0 0 0 0 0 ...
$ Color : int 5 4 5 4 5 4 5 2 5 3 ...
$ ChrNumeric: int 1 1 1 1 1 1 1 1 1 1 ...
Then you can update it and write it back (if you have write permissions), e.g.
pathname19 <- gsub("cytoband", "cytoband,hg19", pathname);
save(cytoband, file=pathname19);
and
# Backup old one, and overwrite existing one
pathname17 <- gsub("cytoband", "cytoband,hg17", pathname);
file.copy(pathname, pathname17);
# Overwrite existing one
file.copy(pathname19, pathname, overwrite=TRUE);
The above is a hack, but should do the trick. If you do the above,
please consider sharing cytoband,hg19.RData here.
/Henrik
On Thu, Jan 12, 2012 at 2:51 PM, Kai <wangz...@gmail.com> wrote:
> Hi Henrik,
>
> I have installed the latest aroma packages. Can you please advice how I can
> setup aroma so that it knows where to look for the correct cytoband
> information when drawing the cytoband in ChromosomeExplorer for displaying
> copy number segmentation results?
>
> I realized that in the old aroma packages that I've been using it got the
> cytoband information from the GLAD package, which hasn't been updated since
> hg17.
>
> Thank you very much.
>
> Best,
> Kai
>
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> 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=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 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] aroma.cn_1.0.0 aroma.affymetrix_2.4.0 affxparser_1.22.0
> [4] aroma.apd_0.2.0 R.huge_0.3.0 aroma.core_2.4.1
> [7] aroma.light_1.22.0 matrixStats_0.4.3 R.rsp_0.7.1
> [10] R.cache_0.5.2 R.filesets_1.1.4 digest_0.5.1
> [13] R.utils_1.9.9 R.oo_1.8.3 R.methodsS3_1.2.1
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
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