Description Usage Arguments Value Examples

Runs the PC-PR2 method on X, an omics matrix of intensities, and Z, the subject metadata to be assessed in the model.

1 | ```
runPCPR2(X, Z, pct.threshold = 0.8)
``` |

`X` |
A matrix of omics data. It is recommended that the data be appropriately scaled and log transformed if necessary. |

`Z` |
A data frame of subject metadata, with the same number of rows as X, whose influence on the omics data is to be assessed. Categorical variables should be coded as factors. |

`pct.threshold` |
The proportion of variability desired to be explained. Defaults to 0.8. |

Returns a list with 6 elements:

`dimensions` |
dimensions of the -omics matrix |

`types` |
data types for each Z-variable |

`threshold` |
the chosen variability to be explained |

`pcn` |
the number of principal components used for the chosen threshold |

`anovaFit` |
ANOVA output for each PC |

`pR2` |
Rpartial2 values for each Z-variable and the overall R2 |

1 2 | ```
output <- runPCPR2(transcripts, Z_metadata)
output$pR2
``` |

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