jaspar: Jaspar 2010 Database
In alyst/MotIV: Motif Identification and Validation

Description Usage Details Source References See Also Examples

Jaspar database and Jaspar score.

1 2	jaspar jaspar.scores

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.

http://jaspar.genereg.net/

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)

generateDBscores, motifMatch

#####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 )