Description Usage Arguments Details Value Author(s) References See Also Examples
Search for motifs matches corresponding to PWM.
1 | motifMatch(inputPWM, database=jaspar, DBscores=jaspar.scores, cc="PCC", align="SWU", top=5, go=1, ge=0.5)
|
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. |
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
.
A motiv
object.
Eloi Mercier <emercier@chibi.ubc.ca>
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
1 2 3 4 5 6 7 8 9 10 11 12 13 | #####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 )
|
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