generateDBScores: Database Scores Functions

In alyst/MotIV: Motif Identification and Validation

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 <[e-mail]>

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=""))

alyst/MotIV documentation built on May 12, 2019, 2:33 a.m.