Dear all,
I have a mapping file from Bowtie from a RNA-seq run against human genome. I
created RangedDataList to represent the mapping coordinates from different
chromosomes, strands and lanes. Now I would like to eliminate the RangedData
entries which have the same IRanges start and end, chromosome number and strand
orientation.
In the following example, entry 1, 3 and 4 have the same chromosome, strand,
start and end, and after the procedure, they should be reduced to one entry. Is
there a function I can use? Or is there some other better ways to represent the
mapping info which include chromosome, strand, star t and end, rather than
RangedData? Thanks.
-Kunbin
> head(sLane[["s_1"]][3])
RangedData with 6 rows and 2 value columns across 1 space
space ranges | strand index
<character> <IRanges> | <factor> <integer>
1 chr1 [223780005, 223780055] | + 6
2 chr1 [ 89018675, 89018725] | - 55
3 chr1 [223780005, 223780055] | + 68
4 chr1 [223780005, 223780055] | + 69
5 chr1 [107921032, 107921082] | - 75
6 chr1 [243086472, 243086522] | - 86
> class(sLane[["s_1"]][3])
[1] "RangedData"
attr(,"package")
[1] "IRanges"
> class(sLane[["s_1"]])
[1] "RangedData"
attr(,"package")
[1] "IRanges"
> class(sLane)
[1] "RangedDataList"
attr(,"package")
[1] "IRanges"
> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu
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] ShortRead_1.6.2 Rsamtools_1.0.1 lattice_0.19-11
[4] Biostrings_2.16.7 GenomicRanges_1.0.1 IRanges_1.6.8
loaded via a namespace (and not attached):
[1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2 tools_2.11.0
>
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