Description Usage Arguments Details Value Author(s) Examples

View source: R/compareTwoDataSets.R

This functions compares the distribution of two sets of RDP-based taxonomic trees using Likelihood-Ratio-Test statistics and a p-value is computed using permutations.

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`data1, data2` |
Data frames in which each column contains the rdp read counts for every taxa given in the row names. |

`numPerms` |
The number of permutation tests to run. |

`parallel` |
When this is 'TRUE' it allows for parallel calculation of the permutations. Requires the package |

`cores` |
The number of parallel processes to run if enableMC is 'TRUE'. |

`maxSteps` |
The maximum number of times to iterate though for the MLE. |

`delta` |
The minimum threshold of change in f to stop the search for the MLE. |

`numBootStraps` |
Deprecated. Replaced with numPerms. |

`enableMC` |
Deprecated. Replaced with parallel. |

Note: Both data sets should be standardized to the same number of reads.

We are interested in assessing whether the distributions from two metagenomic populations are the same or different, which is equivalent to evaluating whether their respective parameters are the same or different. The corresponding hypothesis is given as follows:

*H_{\mathrm{o}}: (g_{1}^{*},τ_{1}) = (g_{2}^{*},τ_{2}) = (g_{0}^{*},τ_{0}) vs H_{\mathrm{A}}: (g_{1}^{*},τ_{1}) \neq (g_{2}^{*},τ_{2}) ,*

where *(g_{0}^{*},τ_{0})* is the unknown common parameter vector. To evaluate this hypothesis we use the likelihood-ratio test (LRT) which is given by,

*λ = -2 \log≤ft(\frac{L(g_{o}^{*},τ_{o};{S_{1n},S_{2m}})}{L(g_{1}^{*},τ_{1};{S_{1n}})+L(g_{2}^{*},τ_{2};{S_{2m}})} \right),*

where *S_{1n}* and *S_{2m}* are the sets containing *n* and *m* random samples of trees from each metagenomic population, respectively.
We assume that the model parameters are unknown under both the null and alternative hypothesis, therefore, we estimate these using the MLE procedure proposed
in La Rosa et al (see reference 2), and compute the corresponding p-value using non-parametric bootstrap.

A p-value for the similarity of the two data sets based on the permutation test.

Patricio S. La Rosa, Elena Deych, Berkley Shands, William D. Shannon

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