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)

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