differentialUptakeKinetics | R Documentation |

This is the main function for fitting functional kinetics to hdx-ms data. Fitting is performed using the minpack library. By default the model will fit a Weibull type model but it is possible to provide a formula for more flexibility. The method using regular expresions to extract the design from the column names or these can be provided.

Computes the residual sum of squares for an `HdxStatModel`

Compute the F statistics

Compute p-value based on the F-test

Empirical Bayes computations

This is the main function for using t-tests for hdx-ms data. The method using regular expresions to extract the design from the column names or these can be provided.

This is the main function for using linear mixed models for hdx-ms data. The method using regular expresions to extract the design from the column names or these can be provided.

This function process the functional fits for hdx-ms data.

differentialUptakeKinetics( object, feature = NULL, design = NULL, formula = NULL, start = list(a = NULL, b = 0.001, d = NULL, p = 1), mycolours = brewer.pal(n = 8, name = "Set2"), maxAttempts = 5 ) computeRSS(object) computeFstat(RSS0, RSS1, d1, d2) computePval(Fstat, d1, d2) hdxEbayes(RSS0, RSS1, d1, d2) ttestUptakeKinetics(object, feature = NULL, design = NULL, formula = NULL) lmUptakeKinetics(object, feature = NULL, design = NULL, formula = NULL) processFunctional(object, params)

`object` |
An object of class |

`feature` |
The feature name of which to fit the model |

`design` |
A character vector indicating replicates, conditions, chargestates, timepoints ete. Default is NULL and design is extract from column names |

`formula` |
The formula used. Default is NULL. |

`start` |
The initial guess for the parameters |

`mycolours` |
A colour palette default uses |

`RSS0` |
Residual sum of squares for null model |

`RSS1` |
Residual sum of squares for altenative model |

`d1` |
The first degrees of freedom for the F-test |

`d2` |
The second degrees of freedom for the F-test |

`Fstat` |
The f-statistic |

`params` |
An object of class |

Returns an instance of class `HdxStatmodel`

A list containing degrees of freedom and residual sums of squares

A list of the relevent statistics

A p-value according to the F-test

p-values and FDR from empirical Bayes method

Returns an instance of class `HdxStatmodel`

Returns an instance of class `HdxStatmodel`

An instance of class `HdxStatRes`

which contains p-values and important
quantities

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