[BioC] ShortRead QA Feature

[Dario Strbenac]

Hello,

I noticed in the report that there is an example like

ShortRead:::.plotCycleBaseCall(perCycle$baseCall)

that produces a graph of the per cycle base calls, but am wondering if there's a function that can easily give you the underlying table used. i.e. The table like :

     Pos  1      2     3      4     ...     ...    36
Base
A         0.224  ...
G         0.276  ...
T         0.251  ...
C         ...    ...
N         ...    ...

I also notice that a readAligned object has 'Alignment mismatch locations' data. Might it be useful to have a similar table to the above table, but with the the different mutations, instead of the bases, as the rows of the table ?

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Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia