readNuPoP {NuPoP} | R Documentation

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

### Description

This function reads in the prediction results generated by `predNuPoP` for specified region.

### Usage

    readNuPoP(file,startPos,endPos)

### Arguments

`file` | the prediction output file name from `predNuPoP` function.
`startPos` | the start position in the DNA sequence for prediction results plotting.
`endPos` | the end position in the DNA sequence for prediction results plotting.

### Value

A dataframe that contains the results from `predNuPoP`. The five columns are `position`: position in the input seqeunce; `P-start`: probability as the start of a nucleosome; `Occu`: nucleosome occupancy, `N/L`: nucleosome (1) or linker (0) based on Viterbi prediction; and `Affinity`: nucleosome binding affinity score.

### Examples

    predNuPoP(system.file("extdata", "test.seq", package="NuPoP"),species=7,model=4)

    ## 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)

[Package NuPoP version 2.0.0 Index]