plotNuPoP: R function for plotting the predicted nucleosome positioning...

In NuPoP: An R package for nucleosome positioning prediction

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)

Example output

NuPoP documentation built on Nov. 8, 2020, 7:09 p.m.