Abhi,
To answer your first question, there is a coverage method for
AlignedRead objects in the ShortRead package. S4 methods can be hard to
find in R's help pages, particularly if the methods for a generic are
stored across multiple packages. When I'm unsure what is around, I use
the showMethods function to get a list of available methods for an S4
generic:
> suppressMessages(library(ShortRead))
> showMethods("coverage")
Function: coverage (package IRanges)
x="AlignedRead"
x="AlignedXStringSet0"
x="IRanges"
x="MaskCollection"
x="MaskedXString"
x="MIndex"
x="numeric"
x="PairwiseAlignedFixedSubject"
x="PairwiseAlignedFixedSubjectSummary"
x="RangedData"
x="RangesList"
x="Views"
From there I use a help command of the form
help("<<generic>>,<<signature>>-method")
> help("coverage,AlignedRead-method")
In that man page you will find information on how to use coverage for an
AlignedRead object.
Once you have the coverage vectors (in the form of an RleList), you can
use the approach Michael outlined for plotting.
Patrick
Michael Lawrence wrote:
On Wed, Dec 2, 2009 at 2:31 PM, Pratap, Abhishek
<[email protected]>wrote:
Hi All
After taking an exciting BioC course at FredHutch recently, I am trying
to dive into BioC world to make more sense of NGS data. I would also
like to thank the entire BioC team present there. You guys were simply
great. I appreciate you all patiently answering tons of questions and
taught some of the cool things we can do with BioC packages.
For my current problem I would like to generate coverage plots for a
small bacterial genome. I have the reads imported as a AlignedRead
object and I am not sure how to proceed next. The help for the
"coverage" method didn't get me very far. I am looking for some pointers
to help me resolve the following questions.
1. How to create a RLE list from the AlignRead object using coverage
method ?
2. Do I need to pack my reference genome as BSgenome data package in
order to do this ? If yes I just have the sequence and no group II mask
file.
3. Finally how to plot a RLE list.
This is a pretty difficult question to answer. Do you want to see all
chromosomes at once (like a karyotype plot)? An overview of entire
chromosomes? Or do you want to explore the data in an interactive genome
browser?
There are many packages in Bioconductor for plotting this sort of data,
including GenomeGraphs and HilbertVis. For genome browsers, there's
rtracklayer and others.
For example, with rtracklayer:
session <- browserSession()
session$coverage <- as(coverage, "RangedData")
Thanks!
-Abhi
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