distanceDyad {ATACseqQC} | R Documentation

## Distance of potential nucleosome dyad

### Description

Calculate the distance of potential nucleosome dyad and the linear model for V.

### Usage

    distanceDyad(vPlotOut, fragLenRanges = c(60, 180, 250), draw = TRUE, ...)

### Arguments

`vPlotOut` | The output of vPlot.
`fragLenRanges` | A numeric vector (length=3) for fragment size of nucleosome free and mono-nucleosome. Default c(60, 180, 250).
`draw` | Plot the results or not. Default TRUE.
`...` | Prameters could be passed to plot.

### Value

an invisible list with distance of nucleosome and the linear model.

### Author(s)

Jianhong Ou

### See Also

vPlot

### Examples

    bamfile <- system.file("extdata", "GL1.bam",
                           package="ATACseqQC")
    library(MotifDb)
    CTCF <- query(MotifDb, c("CTCF"))
    CTCF <- as.list(CTCF)
    library(BSgenome.Hsapiens.UCSC.hg19)
    vp <- vPlot(bamfile, pfm=CTCF[[1]],
         genome=Hsapiens,
         min.score="95%", seqlev="chr1",
         draw=FALSE)
    distanceDyad(vp)

[Package ATACseqQC version 1.12.5 Index]