Description Usage Arguments Value Examples
View source: R/motifSignature.R
extract signatures from multiple motifs by distance calculated from STAMP
1 2 3 4 5 6 7 8 9 10 11 | motifSignature(
pfms,
phylog,
cutoffPval,
groupDistance,
rcpostfix = "(RC)",
min.freq = 2,
trim = 0.2,
families = list(),
sort = TRUE
)
|
pfms |
a list of objects of class pfm |
phylog |
an object of class phylog |
cutoffPval |
pvalue for motifs to merge. |
groupDistance |
maxmal distance of motifs in the same group |
rcpostfix |
postfix for reverse-complement motif names, default: (RC) |
min.freq |
signatures with frequency below min.freq will not be plotted |
trim |
minimal information content for each position of signature |
families |
for each family, the motif number in one signature should only count as 1 |
sort |
sort the signatures by frequency or not. |
an Object of class motifSig
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | if(interactive() || Sys.getenv("USER")=="jianhongou"){
library("MotifDb")
matrix.fly <- query(MotifDb, "Dmelanogaster")
motifs <- as.list(matrix.fly)
motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-",
names(motifs), fixed=TRUE)]
names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "",
gsub("_FBgn[0-9]+$", "",
gsub("[^a-zA-Z0-9]","_",
gsub("(_[0-9]+)+$", "", names(motifs)))))
motifs <- motifs[unique(names(motifs))]
pfms <- sample(motifs, 50)
hc <- clusterMotifs(pfms)
library(ade4)
phylog <- ade4::hclust2phylog(hc)
leaves <- names(phylog$leaves)
pfms <- pfms[leaves]
pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
new("pfm",mat=.ele, name=.name)})
motifSig <- motifSignature(pfms, phylog, cutoffPval=0.0001)
}
|
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