Hi Keith.
On Mon, Jul 29, 2013 at 5:47 PM, Keith Ching <keithchi...@gmail.com> wrote:
> sorry if this has been fixed already..
>
> i'm looking at a gene on chr9 at 138MB. I have segments that go out to
> 140MB.
> But the ChromosomeExplorer plot is truncated at 134MB for a SNP6 chip.
Thanks for spotting this.
>
> Is there somewhere I can configure the plot range for ChromosomeExplorer?
Internally, the annotation data is located as follows:
> gf <- AromaGenomeTextFile$byGenome("Human", verbose=TRUE)
Locating genome annotation file...
Locating genome annotation file...
Genome name: Human
Genome tags:
Genome fullname: Human
Pattern (fmtstr): ^Human,chromosomes(|,.*)*[.]txt$
Pattern (updated): ^Human,chromosomes(|,.*)*[.]txt$
Paths:
NULL
Found file:
C:/Users/hb/R/win-library/3.0/aroma.core/annotationData/genomes/Human/Human,chromosomes.txt
Locating genome annotation file...done
Locating genome annotation file...done
> readDataFrame(gf)
chromosome nbrOfBases nbrOfGenes
1 1 245203898 2968
2 2 243315028 2288
3 3 199411731 2032
4 4 191610523 1297
5 5 180967295 1643
6 6 170740541 1963
7 7 158431299 1443
8 8 145908738 1127
9 9 134505819 1299
10 10 135480874 1440
11 11 134978784 2093
12 12 133464434 1652
13 13 114151656 748
14 14 105311216 1098
15 15 100114055 1122
16 16 89995999 1098
17 17 81691216 1576
18 18 77753510 766
19 19 63790860 1454
20 20 63644868 927
21 21 46976537 303
22 22 49476972 288
23 X 152634166 1184
24 Y 50961097 231
25 M 16569 37
It first searches for the ^Human,chromosomes(|,.*)*[.]txt$ file in
./annotationData/genomes/Human/. If not found there, it then searches
system.file("annotationData/genomes/Human/", package="aroma.core"),
which is the default one. In other words, you can add your own to
./annotationData/genomes/Human/. You can find some alternatives in:
http://aroma-project.org/data/annotationData/genomes/Human/
I think Human,chromosomes,max,20090503.txt(*) would solve your problem.
Cheers,
Henrik
(*) It should work to just copy it, but for unknown reasons you have
to rename it to Human,chromosomes.txt.
>
> thanks,
>
> -keith
>
> using
>
> aroma.light v1.22.0 (2011-10-31)
> aroma.core v2.4.4 (2012-02-01)
>
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