[BioC] questions about Overlap encodings

[Henry Paik]

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.

 > ovenc1
OverlapEncodings of length 2
Loffset Roffset encoding
[1] 4 0 2:jm:af:
[2] 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
?extractSpannedExonRanks
I got
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?

Thanks much!

- Henry

 > sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)

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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C 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] Rsamtools_1.8.4 Biostrings_2.24.1 GenomicFeatures_1.8.1
[4] AnnotationDbi_1.18.0 Biobase_2.16.0 GenomicRanges_1.8.5
[7] IRanges_1.14.2 BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] biomaRt_2.12.0 bitops_1.0-4.1 BSgenome_1.24.0 compiler_2.15.0
[5] DBI_0.2-5 RCurl_1.91-1 RSQLite_0.11.1 rtracklayer_1.16.1
[9] stats4_2.15.0 tools_2.15.0 XML_3.9-4 zlibbioc_1.2.0