hdxstat-functions: This is the main function for fitting functional kinetics to...

In ococrook/hdxstats: Statistical analysis of hydrogen deuterium exchange mass spectrometry

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.

Description

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.

Usage

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)

Arguments

object	An object of class QFeatures
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 brewer.pal.
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 HdxStatModels

Value

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

ococrook/hdxstats documentation built on Sept. 15, 2022, 12:24 p.m.