Description Usage Arguments Value Note Examples

Performs a standard analysis of the data (quality and statistics) from a dataset file.

1 2 3 | ```
mainAnalysis(header, dataset, flagForSameExp, listOfNormalizations, listOfArgs4norm,
listOfStatTests, listOfArgs4stat, multTestAdj, hitScoringVec1, hitScoringVec2,
posNegFlag, flag4Gsea, vecOfChannels, whichOnto)
``` |

`header` |
the header of a dataset file generated with |

`dataset` |
an R data frame generated with |

`flagForSameExp` |
either 0 or 1. If 1, all experiments defined in the column |

`listOfNormalizations` |
a list of the normalization function to apply. Can be |

`listOfArgs4norm` |
a list containing, for each element of |

`listOfStatTests` |
a list of the statistical tests to perform. Can be |

`listOfArgs4stat` |
a list containing, for each element of |

`multTestAdj` |
indicates the p-value correction for multiple testing - one of |

`hitScoringVec1` |
a vector of length 3 indicating (in that order): - scoring according to p-value (0: no, 1: yes) - scoring according to ZScore with ZScore < threshold (0: no, 1: yes), or according to ZScore < threshold and p-value < hitScoringVec2[1] (2) - scoring according to ZScore with ZScore > threshold (0: no, 1: yes), or according to ZScore > threshold and p-value < hitScoringVec2[1] (2). If hitScoringVec1[2] or hitScoringVec1[3] are equal to 2, hitScoringVec1[1] must be equal to one, otherwise p-values will not be computed. |

`hitScoringVec2` |
a vector of length 3 indicating the thresholds for hitscoringvec1 |

`posNegFlag` |
either 0 (no controls available) or 1 (controls available) |

`flag4Gsea` |
Can be: - either 0: No GSEA analysis is performed - or 1: A GSEA analysis is performed for each hit scoring method - or a binary vector that allows to choose which hit scoring method(s) will be used for a GSEA analysis. Hit scoring methods are sorted as follows: first, hits are scored according to the p-values of each test specified in |

`vecOfChannels` |
a character vector containing the names of the channels to be used for quality plots, for example |

`whichOnto` |
one of the three GO hierarchies: |

Generates the html output files ` index.html`

and ` indexnorm.html`

containing the quality analysis of raw and normalized data, respectively, and ` stats.html`

, containing the statistical analysis. If several normalization methods are applied, an `indexnorm`

file is generated after each.

**This function is deprecated and kept only for backwards compatibility.** Please use the ` "rnaiter" `

function instead.

1 2 3 4 5 6 7 | ```
data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")
mainAnalysis(header, dataset, 0, list(controlNorm), list(list(1, 0, "SigIntensity", 1)),
list(Ttest, MannWhitney), list(list("l", 1, "SigIntensity", "GeneName"),
list("l", 1, "SigIntensity", "GeneName")), "none", c(1, 0, 0), c(0.05, 0, 0), 1,
0, c("SigIntensity", "NbCells"), "biological_process")
``` |

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