Hello
What do I need to do to SimpleRleList and Rle before I use them to make a track
with export().
I tried to find help in an earlier thread (WIG from coverage), but I am still
not able to solve the problem.
> cvge_s_1
SimpleRleList: 25 elements
names(25): chr1 chr10 chr11 chr12 chr13 chr14 ... chr7 chr8 chr9 chrM chrX chrY
> cvge_s_1$chr5
'integer' Rle instance of length 180857866 with 15165 runs
Lengths: 181838 20 27419 21 25146 21 18711 19 18247 13 ...
Values : 0 1 0 1 0 1 0 1 0 1 ...
export(cvge_s_1$chr1, "cvge_s_1_chr1.wig")
#This is what I get for chr1:
track name="R Track" type=wiggle_0
variableStep chrom=chr1 span=1
558223 1
558249 1
558777 1
559783 2
559784 3
........
export(cvge_s_1$chr5, "cvge_s_1_chr5.wig")
#This is what I get for all the other chromosomes; it is always chr1:
track name="R Track" type=wiggle_0
chr1 0 4948 0
chr1 4948 4949 2
chr1 4949 4950 3
chr1 4950 4970 4
chr1 4970 4971 3
chr1 4971 4972 2
> sessionInfo()
R version 2.10.0 alpha (2009-10-01 r49909)
x86_64-apple-darwin9.8.0
locale:
[1] en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] HilbertVisGUI_1.3.3 HilbertVis_1.3.4 rtracklayer_1.5.17
[4] RCurl_1.2-0 bitops_1.0-4.1 ShortRead_1.3.36
[7] lattice_0.17-25 BSgenome_1.13.16 Biostrings_2.13.48
[10] IRanges_1.3.87
loaded via a namespace (and not attached):
[1] Biobase_2.5.8 hwriter_1.1 tools_2.10.0 XML_2.6-0
>
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