jaspar2010 {MotIV} | R Documentation

## Jaspar 2010 Database

### Description

Jaspar database and Jaspar score.

### Usage

    jaspar
    jaspar.scores

### Details

Jaspar is a well-known transcription factor database. Version 2010 contents 130 non-redundant matrix of TF binding sites.

The jaspar scores have been computed with Pearson Correlation Coefficient and Smith-Waterman Ungapped alignments.

### Source

http://jaspar.genereg.net/

### References

Albin Sandelin, Wynand Alkema, P\"ar Engstr\"om, Wyeth W. Wasserman and Boris Lenhard, `JASPAR: an open-access database for eukaryotic transcription factor binding profiles`, Nucleic Acids Research(2003)

### See Also

`generateDBscores`, `motifMatch`

### Examples

    #####Database and Scores#####
    path <- system.file(package="MotIV")
    data(jaspar2010)
    data(jaspar2010_scores)

    #####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]