Distance of potential nucleosome dyad

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

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.

See also

vPlot

Author

Jianhong Ou

Examples

bamfile <- system.file("extdata", "GL1.bam",
                       package="ATACseqQC")
library(MotifDb)
#> Loading required package: Biostrings
#> Loading required package: XVector
#> 
#> Attaching package: 'Biostrings'
#> The following object is masked from 'package:base':
#> 
#>     strsplit
#> See system.file("LICENSE", package="MotifDb") for use restrictions.
CTCF <- query(MotifDb, c("CTCF"))
CTCF <- as.list(CTCF)
library(BSgenome.Hsapiens.UCSC.hg19)
#> Loading required package: BSgenome
#> Loading required package: rtracklayer
vp <- vPlot(bamfile, pfm=CTCF[[1]],
     genome=Hsapiens,
     min.score="95%", seqlev="chr1",
     draw=FALSE)
distanceDyad(vp)