Description Usage Arguments Details Value Author(s) Examples

View source: R/pairedCompareTwoDataSets.R

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

1 2 | ```
pairedCompareTwoDataSets(data1, data2, numPerms = 1000, parallel = FALSE,
cores = 3, maxSteps=50, delta=10^(-6))
``` |

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

`numPerms` |
Number of permutations. In practice this should be at least 1,000. |

`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 parallel 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. |

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

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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