refineFunction {methylscaper} | R Documentation

## Refinement

### Description

Reorders a subset of the methylation data.

### Usage

    refineFunction(orderObject, refineStart, refineEnd, Method = "PCA")

### Arguments

`orderObject` | An object of class `orderObject`, generated with the `initialOrder` function.
`refineStart` | The index of the first sample (row) used in the refinement.
`refineEnd` | The index of the last sample (row) used in the refinement.
`Method` | The seriation method used to perform the refinement.

### Value

The refinement reorders the cells/molecules (rows) between the indicated start and end positions. The function returns the new complete ordering with the refinement applied.

### Examples

    data(singlemolecule_example)

    orderObj <- initialOrder(singlemolecule_example, Method = "PCA")
    # reordering the first 50 cells/molecules (rows)
    orderObj$order1 <- refineFunction(orderObj, 1, 50)

[Package methylscaper version 1.0.1 Index]