generateDBScores {MotIV} | R Documentation

## Database Scores Functions

### Description

This functions are used to generate scores of a PWM database.

### Usage

    generateDBScores(inputDB,cc="PCC",align="SWU",nRand=1000,go=1,ge=0.5)
    readDBScores(file)
    writeDBScores(x, file)

### Arguments

`inputDB` | A list of PWM corresponding to the database.
`cc` | The metric name to be used :
`align` | The Alignment method to be used.
`go` | Gap open penality.
`ge` | Gap extension penality.
`nRand` | The number of random PWM to be generated. The more higer it is, the more accurate score will be.
`file` | A character string naming a file.
`x` | A numeric matrix corresponding to a score.

### Details

The score reflects the biais of the database. It is used to compute more precisely e-value alignments.

`generateDBScores` : Based on database properties (suchs as length, zero rate, invariant colums ), nRand matrix are generated. A score is calculated for each matrix length with the specified alignment method and metric.

The `score` is associated to a database and a alignment method and metric so you don't have to generate it each time you use the same database. Use the `writeDBScores` and `readDBScores` instead. `readDBScores` : Read a score file. `writeDBScores` : Write a score file.

### Value

A numeric matrix. Columns correspond respectively to the first matrix length, second matrix length, variance, mean, matrix number, distance min and max.

### Warning

Because of each matrix is compare to each other, computing time is exponential. You should be aware of this fact before provided a high nRand. 5000 is a good time/accuracy rate choice.

### Author(s)

Shaun Mahony, modified by Eloi Mercier <emercier@chibi.ubc.ca>

### References

Sandelin,A. and Wasserman,W.W. (2004) `Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics`. J. Mol. Biol., 338, 207/215.

### See Also

'readDBScores', 'writeDBScores'

### Examples

    #####Database and Scores#####
    path <- system.file(package="MotIV")
    jaspar <- readPWMfile(paste(path,"/extdata/jaspar2010.txt",sep=""))
    #jaspar.scores <- generateDBScores(inputDB=jaspar,cc="PCC",align="SWU",nRand=1000)
    #writeDBScores(jaspar.scores,paste(path,"/extdata/jaspar_PCC_SWU.scores",sep=""))
    jaspar.scores <- readDBScores(paste(path,"/extdata/jaspar2010_PCC_SWU.scores",sep=""))

[Package MotIV version 1.42.0 Index]