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Microbial Community Alignment Class

class-MiCoAl.Rmd

Microbial Community Alignment Class

  • Takes a number of MiCo objects as input (? list or …) and an additional argument to specify if a pairwise alignment of the communities is desired.
  • The default is to align all communities against each other
  • if pairwise = TRUE all unique pairwise combinations are aligned.
  • Should the alignment be calculated upon the creation of the object or should it be calculated on demand?

Methods

A variety of methods can be called on a MiCoAl object. The output of the methods has to be assigned back to the variable containing the object to persist.

  • clusterAlignment: Takes a MiCoAl object as input and an additional argument to specify the clustering algorithm to be used, only works on MiCoAl objects that have undergone a pairwise alignment.

Identity

A value which gives a scalar value to represent the identity between two communities.

α∑i=1n(∑Ci−α)+α \frac{\alpha}{\sum\limits_{i = 1}^{n}(\sum C_i - \alpha) + \alpha}

Contents

  • Communities hash/list containing the MiCo objects
  • Alignment hash:
    • overall alignment matrix (binary)
    • hash for each level calculated (### how many levels?)
      • alignment matrix
      • longest connected components for each level
      • how to score alignments with more communities more highly?
      • how to figure out the connecctedness for parts of the alignment in whicch there are less communities represented than in the overall alignment?