estimateFragmentCenters {MMDiff2} | R Documentation

## estimate center of fragments

### Description

This function computes average shifts between forward and reverse strand and applies it to estimate fragment centers.

### Usage

    estimateFragmentCenters(MD, shift = NULL, draw.on = FALSE)

### Arguments

`MD` | DBAmmd Object. This Object can be created using `DBAmmd()`.
`shift` | can be set if the offset between forward and reverse strand is known (e.g. 1/2 median fragment size). In this case shift will not be estimated (DEFAULT: NULL)
`draw.on` | plot scatterplots for counts on forward vs reverse strand and histograms of determined shifts (DEFAULT: FALSE)

### Value

DBAmmd object with updated slots `Reads` and `MetaData`.

### See Also

`DBAmmd`, `getPeakReads`, `compHists`

### Examples

    ## Example using a small data set provided with this package

    data("MMD")
    MMD.1 <- estimateFragmentCenters(MMD)

    # To access centers of fragments:
    Reads.C <- Reads(MMD.1,'Center')

    # To access the determined shifts for each sample:
    meta <- metaData(MMD.1)
    meta$AnaData$Shifts

[Package MMDiff2 version 1.18.0 Index]