plotNuPoP {NuPoP} | R Documentation

## R function for plotting the predicted nucleosome positioning map and nucleosome occupancy map

### Description

This function produces two plots from a specified region based on the prediction results from function `predNuPoP`. The first plot is the nucleosome occupancy (grey color). In the second plot, in addition to the occupancy, Viterbi prediction (red rectangle) and the posterior probability for a position to be the start of a nucleosome (blue color) are superimposed.

### Usage

    plotNuPoP(predNuPoPResults)

### Arguments

`predNuPoPResults` | NuPoP prediction results from predNuPoP function. It must be a data frame read in by readNuPoP function.

### Value

`plotNuPoP` outputs two plots: the nucleosome occupancy score map and Viterbi optimal nucleosome positioning map together with posterior probability for a position to be the start of a nucleosome.

### Examples

    library(NuPoP)

    ## the prediction results are stored in the current working directory
    ## the user should replace "system.file("extdata","test.seq_Prediction4.txt",package="NuPoP")"
    ## by the actual path and file name generated from prediction.
    temp=readNuPoP(system.file("extdata","test.seq_Prediction4.txt",package="NuPoP"),startPos=1,endPos=5000)
    plotNuPoP(temp)

[Package NuPoP version 1.40.0 Index]