motifMatch {MotIV} | R Documentation

## Motifs Matches Analysis

### Description

Search for motifs matches corresponding to PWM.

### Usage

      motifMatch(inputPWM, database=jaspar, DBscores=jaspar.scores, cc="PCC", align="SWU", top=5, go=1, ge=0.5)

### Arguments

`inputPWM` | A list of PWM.
`database` | A list of PWM corresponding to the database.
`DBscores` | A matrix object containing the scores associated to the database.
`cc` | The metric name to be used
`align` | The Alignment method to be used.
`top` | The number of identified transcription factors per motif.
`go` | Gap open penality.
`ge` | Gap extension penality.

### Details

For a set of PWMs given by `inputPWM`, this function realizes alignments with each motif of the `database` and returns the `top` best motifs. If no `database` is provided, the function will use jaspar by loading data(jaspar2010). If no `DBscores` is given, jaspar.scores from data(jaspar2010_scores) will be used.

The e-value is computed according the matric name `cc` and is corrected by the `DBscores`.

### Value

A `motiv` object.

### Author(s)

Eloi Mercier <emercier@chibi.ubc.ca>

### References

S Mahony, PE Auron, PV Benos, `DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies`, PLoS Computational Biology (2007) 3(3):e61

### See Also

`generateDBScores`

### Examples

    #####Database and Scores#####
    path <- system.file(package="MotIV")
    jaspar <- readPWMfile(paste(path,"/extdata/jaspar2010.txt",sep=""))
    jaspar.scores <- readDBScores(paste(path,"/extdata/jaspar2010_PCC_SWU.scores",sep=""))

    #####Input#####
    data(FOXA1_rGADEM)
    motifs <- getPWM(gadem)
    motifs.trimed <- lapply(motifs,trimPWMedge, threshold=1)

    #####Analysis#####
    foxa1.analysis.jaspar <- motifMatch(inputPWM=motifs,align="SWU",cc="PCC",database=jaspar,DBscores=jaspar.scores,top=5)
    summary(foxa1.analysis.jaspar )

[Package MotIV version 1.40.0 Index]