Ridges {SigWinR} | R Documentation |
Use SigWin to calculate rigdges given a certain set of window sizes.
Ridges(s, window.size, pos=NULL,pval = 0.05, antiRidge = FALSE, adjust.method = "BH", min.sup = length(window.size),resolution=400)
s |
input sequence |
window.size |
vector of window sizes (only odd windowsizes are considered) |
pos |
position of samples in input sequence |
pval |
p-value |
antiRidge |
Look for anti ridges |
adjust.method |
Multiple testing adjustment |
min.sup |
The minimum number of window.sizes which have to find a ridge for a certain point to consider it a ridge |
resolution |
Resolution of the ridge calculation (for localized SigWin only) |
A data frame is returned containing a row for each found ridge and the start and end positions in the columns
w.c.deLeeuw@uva.nl
SigWin,Ridgeogram
lseq <- c(rnorm(200),rnorm(100,-1),rnorm(50),rnorm(50,4.0),rnorm(100)) ridgelist <- list(Ridges(lseq,seq(45,65,by=2)),Ridges(lseq,seq(45,65,by=2),antiRidge=TRUE)) RidgePlot(ridgelist,lseq,labels=c("ridges","anti-ridges"),col=c("#88FF88","#FF8888")) lseq <- c(rnorm(100),rnorm(100,3),rnorm(300),rnorm(100,-3),rnorm(200),rnorm(50,4.0),rnorm(100)) rg <- Ridgeogram(lseq) #find 5 window sizes in which lowest p-value occur win.neg <- 1+2*order(apply(log(rg$low),2,min))[1:5] win.pos <- 1+2*order(apply(log(rg$high),2,min))[1:5] rp <- Ridges(lseq,win.pos,pval=0.01) rn <- Ridges(lseq,win.neg,antiRidge=TRUE,pval=0.01); RidgePlot(list(rp,rn),lseq,ptitle="Most significant ridges", labels=c("ridges","anti-ridges"),col=c("#CCFFCC","#FFCCCC"))