Joseph,
There is a short term answer and a long term answer to that question.
The short term answer is below. The long term answer is that the
GenomicFeatures infrastructure is undergoing rapid changes and so you
should use it with caution over the next 2-4 weeks. If you run into any
issues or have any feature requests, don't hesitate to e-mail the list.
library(ShortRead)
sp <- SolexaPath(system.file("extdata", package="ShortRead"))
ap <- analysisPath(sp)
aligns <- readAligned(ap, "s_2_export.txt", "SolexaExport")
aligns <- aligns[!is.na(position(aligns))]
levels(ali...@chromosome) <- gsub("\\.fa$", "", levels(chromosome(aligns)))
alignRanges <-
GRanges(seqnames = chromosome(aligns),
ranges = IRanges(position(aligns), width = width(aligns)),
strand = as.character(strand(aligns)))
alignRanges
GRanges with 406 ranges and 0 values columns
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
1 chr17 [ 69345321, 69345355] - |
2 chr18 [ 54982866, 54982900] + |
3 chr12 [ 80537786, 80537820] - |
4 chr10 [117148563, 117148597] - |
5 chr9 [ 9192755, 9192789] - |
6 chr1 [ 3393025, 3393059] + |
7 chr19 [ 4786365, 4786399] - |
8 chr2 [ 98506741, 98506775] - |
9 chr9 [ 3026723, 3026757] + |
10 chr8 [129798321, 129798355] + |
On 2/27/10 7:29 PM, joseph wrote:
Hello
My goal is to identify the genes associated with the reads in my AlignedRead
object using GenomicFeatures package.
Can you please show me how to make the GRanges object from the AlignedRead?
Joseph Dhahbi
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