jaspar2010 {MotIV} | R Documentation |
Jaspar database and Jaspar score.
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 )