iPE::Levels(3)

NAME
iPE::Levels - A class to keep track of the gc levels of a sequence.

DESCRIPTION
This object will take in a DNA sequence and based on the window size will create non-overlapping windows of the G+C% contained in each window. The owning window of any base can be accessed from that base.

FUNCTIONS

new (members)
    new creates a new Levels object. The following are needed in the members hash reference:

    seqRef
        The DNA sequence as a string reference.

    windowSize
        The size of the nonoverlapping windows to detect gc content with.

    setLevels (sequence)
        Sets the levels for the current sequence. Adds to the cumulative total the levels thus far.

    normalizeTotals
        Normalizes the total levels for use of the cumulative totals.

    cumulative
        Gets the cumulative distribution of DNA characters for all sequences seen.

    gc (pos)
        Return the isochore GC content at the position given on the forward strand. The method for determining this is through a window size. The position is fitted to the nearest window as defined by the global isochoreWindow option in iPE.

    levels_at (pos)
        Return a hash reference to the content at the given position on the forward strand. Each key in the hash reference is one of the letters (A,C,G,T) and represents the levels of that letter.

SEE ALSO
iPE

AUTHOR
Bob Zimmermann (rpz@cse.wustl.edu)

POD ERRORS
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Around line 138:
    You forgot a '=back' before '=head1'