BiSeq (version 1.12.0)

logisticRegression: Estimates and tests a group factor

Description

It is used to fit a linear model on the log odds of each (smoothed) methylation level. The first independent variable in formula is tested to be unequal to zero.

Usage

logisticRegression(formula, link, object, mc.cores)

Arguments

formula

An object of class formula. For the first independent variable the p-value and the effect on methylation is returned.

link

A character specifying the link function. Currently, "logit", "probit", "cloglog", "log", "loglog" are supported.

object

A BSrel object.

mc.cores

Passed to mclapply.

Value

A data.frame containing the position, chromosome, P value, estimated methylation level in group 1 and group 2 and methylation difference of group 1 and group 2.

See Also

mclapply, glm

Examples

data(predictedMeth)

logisticResults <- logisticRegression(formula = ~group, link = "logit",
                                      object = predictedMeth)