Description Usage Details Source References See Also Examples
Jaspar database and Jaspar score.
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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)
1 2 3 4 5 6 7 8 9 10 11 12 13 | #####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 )
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