[BioC] questions about Overlap encodings
hp65 at med.harvard.edu
Tue May 8 18:18:19 CEST 2012
Hi List and Hervé,
First of all, thank you very much for all your hard work on Bioconductor.
I have some questions about OverlapEncodings
1. OverlapEncodings object looks like below.
OverlapEncodings of length 2
Loffset Roffset encoding
 4 0 2:jm:af:
 4 0 2:jm:af:
Under encoding, 2 is the number of exons in this junction. What do jm
and af (or i, am, gm,...) mean?
2. How could I know which exons are involved to a junction? or how could
I know the exon ranks from OverlapEncodings?
extractSpannedExonRanks function is not implemented?
When I did
No documentation for ‘extractSpannedExonRanks’
3. How could I know the number of unique reads on unique junctions?
I can filter to get the unique match for each read before bioC analysis.
But to quantify the reads on the junctions, I think I need the count of
the unique read_id on unique junction?
I am learning all these from "Overlap encodings" vignette. Are there any
other documentation to learn more about this?
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
 LC_PAPER=C LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 Rsamtools_1.8.4 Biostrings_2.24.1 GenomicFeatures_1.8.1
 AnnotationDbi_1.18.0 Biobase_2.16.0 GenomicRanges_1.8.5
 IRanges_1.14.2 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
 biomaRt_2.12.0 bitops_1.0-4.1 BSgenome_1.24.0 compiler_2.15.0
 DBI_0.2-5 RCurl_1.91-1 RSQLite_0.11.1 rtracklayer_1.16.1
 stats4_2.15.0 tools_2.15.0 XML_3.9-4 zlibbioc_1.2.0
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