reformData {DMRMark} R Documentation

## Reform M-values into a two-column matrix.

### Description

Reform M-values into a matrix with two columns representing matched control and case groups. It concatenate M-values pair-by-pair based on the design matrix.

### Usage

reformData(mv, pd=NULL)


### Arguments

 mv The input M-values matrix, NA is not allowed. pd A design matrix, which can be generated by 'stats::model.matrix'. If the M-values are totally paired or single paired, just leave it to be NULL.

### Value

A matrix with two columns representing matched control and case groups. If a sample has no paired sample in another group (say group B), then the values in group B will be represented by NA.

### Author(s)

Linghao SHEN <sl013@ie.cuhk.edu.hk>

### Examples


# Assume the values come from Tumor is 10 larger than those from Normal.

# The case with totally paired data
mv1 <- matrix(1:20,5)
reformData(mv1)

# The case with One more sample from Tumour group
# The second Tumour sample is the extra one
mv2 <- matrix(1:25,5)
mv2[,2] <- mv2[,2] + 5
patient <- factor(c(1,3,1:3))
type = c(rep("Normal",2),rep("Tumour",3))
pd <- model.matrix(~patient + type + 0)
reformData(mv2, pd)


[Package DMRMark version 1.1.1 Index]