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MicrobiomeFunctionAlignment Class

class-MicrobiomeFunctionAlignment.Rmd

Microbial Community Alignment Class

  • Clarify how the Alignment is represented primarily. Will it also be a TSE object?

  • Could use the assays to store each alignment, this would allow for quick calculation of the depth and breadth as well.

  • Decide on metrics to include in the alignment

  • in how many communities is any given species?

  • How to go about the multiscale entropy?

  • How do we maximise for community overlap in the alignment?

  • What happens if we have completley disconnected grpahs? how do we align with and without gaps?

  • To what extent should the alignment be interactive?

  • Takes a number of MicrobiomeFunction 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 MicrobiomeFunctionAlignment object. The output of the methods has to be assigned back to the variable containing the object to persist.

  • clusterAlignment: Takes a MicrobiomeFunctionAlignment object as input and an additional argument to specify the clustering algorithm to be used, only works on MicrobiomeFunctionAlignment 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 MicrobiomeFunction 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?