distanceDyad: Distance of potential nucleosome dyad
In jianhong/ATACseqQC: ATAC-seq Quality Control

distanceDyad

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

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)

jianhong/ATACseqQC documentation built on March 19, 2024, 8:30 a.m.