Description Usage Arguments Details Author(s) Examples
Set of functions to perfom clustering of PWMs.
1 2 3 | motifDistances(inputPWM, DBscores=jaspar.scores, cc="PCC", align="SWU", top=5, go=1, ge=0.5)
motifHclust(x,...)
motifCutree(tree,k=NULL, h=NULL)
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inputPWM, DBscores, cc, align, top, go, ge |
Option for the PWMs distances computation. Refere to |
x,... |
Arguments to pass to the hclust function. See |
tree, k, h |
Arguments to pass to the cutree function. See |
This function are made to perform motifs clustering.
The ‘motifDistances’ function computes the distances between each pair of motifs using the specified alignment.
The ‘motifHclust’ and ‘motifCutree’ functions are simple redefinition of ‘hclust’ and ‘cutree’.
Eloi Mercier <emercier@chibi.ubc.ca>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | #####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)
#####Clustering#####
d <- motifDistances(getPWM(foxa1.analysis.jaspar))
hc <- motifHclust(d)
plot(hc)
f <- motifCutree(hc, k=2)
foxa1.combine <- combineMotifs(foxa1.analysis.jaspar, f, exact=FALSE, name=c("Group1", "Group2"), verbose=TRUE)
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