Description Usage Arguments Details Value Note Author(s)

This function applies a statistical test either a correlation (spearman, pearson), wilcoxon or t.test as a function of a given phenotype. It will return a matrix of probabilities p and q values along with the correlation coefficient or the enrichment variable when a binary parameter.

1 2 |

`data` |
: frequency matrix with gene_ids in the rownames |

`trait` |
: a vector with the trait to test, binary or numerical variable |

`type` |
: a character string indicating the type of test to be applied |

`restrict` |
: an optional logical vector to select a subset of the samples to perform the test default restrict = rep(TRUE, ncol(data)) ie all the samples are selected |

`multiple.adjust` |
: type of multiple adjustment default is "BH" i.e. Benjamini & Hochberg method |

`paired` |
: logical with default FALSE wether the test should be paired or not |

`debug` |
: default FALSE, when TRUE the progress is printed each 1000 steps |

`testRelations`

a matrix with analytical results (correlation tests) indicating rho, rho2, p and q values for each parameter tested

New addon taking into account a trait for correlation, when it is a two class variable with the same number of elements a correlation between both groups is performed

Edi Prifti & Emmanuelle Le Chatelier

momr documentation built on May 19, 2017, 3:35 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

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