Hello,
I have a rather simple question that involves GenomicRanges' design.
Basically, I have a GRanges object where all the elements are from the
undefined "*" strand. I just want to resize them to get the 1st (from left
to right) base. However, I'm not able to do so with the "resize" function
even when specifying fix = "start" as it uses the fix = "center" method. Is
this the desired performance? I have 2 workarounds, but I'm puzzled as the
"flank" function actually uses the start (left to right) when elements are
from the "*" strand. Is there a quicker way to do this or should I stick to
the flank + shift workaround?
Thank you and greetings,
Leonardo
> testGR <- GRanges( seqnames = rep("test", 3), ranges = IRanges ( start =
c(10,100,1000), width = c(10, 100, 1000)), strand = Rle(strand(c("+","-")),
c(1,2)) )
> testGR
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] test [ 10, 19] + |
[2] test [ 100, 199] - |
[3] test [1000, 1999] - |
seqlengths
test
NA
> resize(testGR, 1, fix="start")
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] test [ 10, 10] + |
[2] test [ 199, 199] - |
[3] test [1999, 1999] - |
seqlengths
test
NA
> testGR2 <- GRanges( seqnames = rep("test", 3), ranges = IRanges ( start =
c(10,100,1000), width = c(10, 100, 1000)), strand = Rle(strand(c("*")),
c(3)) )
> testGR2
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] test [ 10, 19] * |
[2] test [ 100, 199] * |
[3] test [1000, 1999] * |
seqlengths
test
NA
> resize(testGR2, 1, fix="start")
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] test [ 14, 14] * |
[2] test [ 149, 149] * |
[3] test [1499, 1499] * |
seqlengths
test
NA
> testGR3 <- GRanges ( seqnames = seqnames(testGR2), ranges = IRanges( start
= start(testGR2), width = 1), strand = strand(testGR2) )
>
> testGR3
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] test [ 10, 10] * |
[2] test [ 100, 100] * |
[3] test [1000, 1000] * |
seqlengths
test
NA
>
> testGR4 <- shift(flank( testGR2, 1), 1)
> testGR4
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] test [ 10, 10] * |
[2] test [ 100, 100] * |
[3] test [1000, 1000] * |
seqlengths
test
NA
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-09-08 r52880)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicRanges_1.1.25 IRanges_1.7.33
loaded via a namespace (and not attached):
[1] tools_2.12.0
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