pvalueBetaReg: Infer sample-specific hypermethylation

In HengPan2007/MethSig: DNA Methylation Drivers Inference

Description

Expected DHcR is estimated through beta regression model and expected DHcR is tested against observed DHcR to evalute if there is promoter hypermethylation.

Usage

pvalueBetaReg(formula, data)

Arguments

formula	An object of class "formula" (or one that can be coerced to that class): a symbolic description of the model to be fitted. The name of y variable should be DHcR_Tumor_Beta.
data	A data frame object generated by makeInputMatrix containing following columns: Id, Hugo, Covariates included in matCV, PDR_Tumor, Depth_Tumor, CpGs_Tumor and DHcR_Tumor. An example can be loaded by using invisible(inputMat).

Value

A data frame summarizing information of sample-specific hypermethylation inference. Addtional columns are added to the input matrix.

• DHcR_Tumor_Beta: Transformed data of DHcR_Tumor (from [0, 1] to (0, 1))

• Beta_Response: Response value estimated by beta regression

• Beta_Precision: Precision value estimated by beta regression

• Pvalue: P-value of sample-specific hypermethylation inference

Examples

pvalueBetaReg(formula = 'DHcR_Tumor_Beta~DHcR_Normal+PDR_Normal+GEXP_Normal+Reptime+PDR_Tumor+Depth_Tumor+CpGs_Tumor',
              data = invisible(inputMat))

HengPan2007/MethSig documentation built on Aug. 1, 2020, 4:52 a.m.