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R/postPING.R
In PING: Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Defines functions
processDup
PostDup
PostSigma
PostDelta
PostError
postPING
Documented in
postPING
# Usage: Post-process PING results Input: ping: PING result before post-process seg.boundary: a data.frame object gives
# the cutting points of segmentations (cut obtained in segmentation step, not the min/max of reads) if seg.boundary is
# give, all predictions outside of boundary should be removed. This data frame contains 3 columns 'ID' for id of
# candidate regions and 'seg.start'/'seg.end' for start/end points of segment min.dist=100, minimum distance of two
# adjacent nucs, smaller than that will be treated as duplicated prediction on boudary postPING <- function(ping, seg,
# rho=8, makePlot=FALSE, datname='', seg.boundary=NULL, DupBound=NULL, IP=NULL,
# FragmentLength=100,mart=NULL,sigmaB2=2500,rho1=0.8,alpha1=20,alpha2=100,beta2=100000,xi=160, PE=FALSE, min.dist=100,
# lambda=-0.000064) postPING <- function(ping, seg, rho=8,
# sigmaB2=2500,rho1=0.8,alpha1=20,alpha2=100,beta2=100000,xi=150, min.dist=100, lambda=-0.000064)
#' Post process Estimation of binding site positions obtained from PING
#'
#' Post process Estimation of binding site positions obtained from PING. Refit
#' mixture models with stronger prior in candidate regions contain potential
#' problems, and then convert final result into dataframe.
#'
#' @param ping A \code{pingList} object containing estimation of nucleosome
#' positions as returned by the \code{PING} function.
#' @param seg An object of class \code{segmentReadsList} containing the results
#' for all pre-processed regions as returned by \code{segmentReads}.
#' @param paraEM A \code{list} of parameters for the EM algorithm. The default
#' parameters should be good enough for most usages.
#' @param minK An \code{integer}.The minimum number of binding events per region.
#' If the value is 0, the minimum number is automatically calculated.
#' @param maxK An \code{integer}. The maximum number of binding events per region.
#' If the value is 0, the maximum number is automatically calculated.
#' @param tol A \code{numeric}. The tolerance for the EM algorithm.
#' @param B An \code{integer}. The maximum number of iterations to be used.
#' @param mSelect A \code{character} specifying the information criteria to be
#' used when selecting the number of binding events. Default="AIC3"
#' @param mergePeaks A \code{logical} stating whether overlapping binding events should be picked.
#' @param mapCorrect A \code{logical} stating whether mappability profiles should
#' be incorporated in the estimation, i.e: missing reads estimated.
#' @param paraPrior A \code{list} of parameters for the prior distribution. The
#' default parameters should be good enough for most usages.
#' @param xi An \code{integer}. The average DNA fragment size.
#' @param rho An \code{integer}. A variance parameter for the average DNA fragment size distribution.
#' @param alpha An \code{integer}. First hyperparameter of the inverse Gamma
#' distribution for sigma^2 in the PICS model
#' @param beta An \code{integer}. Second hyperparameter of the inverse Gamma
#' distribution for sigma^2 in the PING model
#' @param lambda An \code{integer}. The lambda control Gaussian Markov Random
#' Field prior on the distance of adjacent nucleosomes, we do not recommend user
#' change the default value.
#' @param dMu An \code{integer}. Our best guess for the distance between two
#' neighboring nucleosomes.
#' @param rho2,sigmaB2,alpha2,beta2 Integer values, the parameters in the
#' prior of mixture models to be re-fitted.
#' @param min.dist The minimum distance of two adjacent nucleosomes predicted
#' from different candidate regions, smaller than that will be treated as
#' duplicated predictions for the same nucleosomes.
#' @param score A \code{numeric}. The score threshold used when calling \code{FilterPING}.
#' @param dataType A \code{character} that can be set to use selected default
#' parameters for the algorithm.
#' @param nCores An \code{integer}. The number of cores that should be used in
#' parallel by the function.
#' @param makePlot A \code{logical}. Plot a summary of the output.
#' @param mart,seg.boundary,DupBound,datname Plotting parameters and options.
#' @param IP A \code{GRanges} object. The reads used in segmentation process.
#' @param FragmentLength An \code{integer}. The length of XSET profile extension
#'
#' @note
#' Based on our experiemt on a few real data sets, we suggestion to use following
#' values of parameters. For sonication data we use rho1=1.2; sigmaB2=6400;
#' rho=15; alpha1=10; alpha2=98; beta2=200000. For MNase data we use rho1=3;
#' sigmaB2=4900; rho=8; alpha1=20; alpha2=100; beta2=100000. The value of xi
#' depends on specs of sample, since that affect the length of linker-DNA.
#' For example, we use xi=160 for yeast and xi=200 for mouse.
#'
#' @return A \code{data.frame} containing the estimated binding site positions
#'
#' @seealso PING, plotSummary
#'
#' @importFrom PICS setParaEM setParaPrior
#' @export
postPING <- function(ping, seg, rho2 = NULL, sigmaB2 = NULL, alpha2 = NULL,
beta2 = NULL, min.dist = 100, paraEM = NULL,
paraPrior = NULL, score = 0.05, dataType = "MNase",
nCores = 1, makePlot = FALSE, FragmentLength = 100,
mart = NULL, seg.boundary = NULL, DupBound = NULL,
IP = NULL, datname = "") {
if (length(ping) != length(seg)) {
stop("The length of `ping' and `seg' arguments are different. `seg' must be the same used when calling PING.")
}
PE <- ping@PE
if (length(paraPrior) != 6) {
if (isTRUE(PE))
paraPrior <- setParaPrior(dataType = dataType, PExi = seg@paraSW$xi) else paraPrior <- setParaPrior(dataType = dataType)
}
if (length(paraEM) != 7) {
paraEM <- setParaEM(dataType = dataType)
}
if (length(c(rho2, sigmaB2, alpha2, beta2)) != 4 | !is.numeric(c(rho2, sigmaB2, alpha2, beta2))) {
if (tolower(dataType) == "mnase") {
message("Using default refitting parameters for MNase data, for sonicated data, set the argument dataType")
rho2 <- 8
sigmaB2 <- 4900
alpha2 <- 100
beta2 <- 1e+05
} else if (tolower(dataType) == "sonicated") {
message("Using default refitting parameters for sonicated data")
rho2 <- 15
sigmaB2 <- 6400
alpha2 <- 98
beta2 <- 2e+05
} else {
stop("Invalid dataType, must be either 'MNase' or 'sonicated'")
}
}
# 'Sonication': {rho1=1.2; sigmaB2=6400;rho=15;alpha1=10; alpha2=98; beta2=200000} MNase: {rho1=3; sigmaB2=4900; rho=8;
# alpha1=20; alpha2=100; beta2=100000} produce the PING result dataframe and add rank info
ps = as(ping, "data.frame")
# ps=as.df(ping,seg)
if (!is.null(seg.boundary)) {
temp <- merge(ps, seg.boundary, all.x = T, all.y = FALSE, by = "ID")
idx <- ((temp$mu >= temp$seg.start) & (temp$mu <= temp$seg.end))
ps <- ps[idx, ]
}
ps = ps[order(ps$score, decreasing = T), ]
ps$rank = 1:nrow(ps)
ps1 = PostError(ps = ps, ping = ping, seg = seg, makePlot = makePlot, datname = datname, DupBound = DupBound, IP = IP,
FragmentLength = FragmentLength, paraEM = paraEM, paraPrior = paraPrior, nCores = nCores, rho2 = rho2)
ps2 = PostDelta(ps = ps1, ping = ping, seg = seg, makePlot = makePlot, datname = datname, DupBound = DupBound, IP = IP,
FragmentLength = FragmentLength, paraEM = paraEM, paraPrior = paraPrior, nCores = nCores, rho2 = rho2, sigmaB2 = sigmaB2,
score = score)
ps3 = PostSigma(ps = ps2, ping = ping, seg = seg, rho2 = rho2, makePlot = makePlot, datname = datname, DupBound = DupBound,
IP = IP, FragmentLength = FragmentLength, mart = mart, sigmaB2 = sigmaB2, paraEM = paraEM, paraPrior = paraPrior,
nCores = nCores, alpha2 = alpha2, beta2 = beta2, score = score, PE = PE)
PS = PostDup(ps = ps3, ping = ping, seg = seg, rho2 = rho2, paraPrior = paraPrior, nCores = nCores, PE = PE, min.dist = min.dist)
return(PS)
}
######################################################## Usage: Post-process PING results to solve the singularity problem of PING model fitting Input: ping: PING output
######################################################## before post-process seg: PING segmentation results rho: hyper-parameter in prior, which control strengh of prior on
######################################################## 'delta', larger rho means more confidence on prior guess of 'delta' ps: dataframe converted from ping output, which
######################################################## might be already post-processed makePlot: indicator of whether or not make plots of pre- and post-processed PING
######################################################## results in pdf files. Following input parameters is only useful when we need to make plots in pdf files datname:
######################################################## name of datasets, which only used as plot file name DupBound: max # of allowed duplicated reads, which is only used
######################################################## in plot IP: the reads in IP data in 'GenomeData' format FragmentLength: the length of XSET profile extention Output
######################################################## PS: the post-processed PING results used to replace input 'ps' PostError <- function(ps, ping, seg, rho=8,
######################################################## makePlot=FALSE, datname='', DupBound=NULL, IP=NULL, FragmentLength=100,rho1,alpha1,xi, PE,lambda)
#' @importFrom PICS code
PostError <- function(ps, ping, seg, rho2 = 8, makePlot = FALSE, datname = "", DupBound = NULL, IP = NULL, FragmentLength = 100,
paraEM, paraPrior, nCores) {
idxE = which(code(ping) != "")
if (length(idxE) == 0) {
print("No regions with pingerror")
PS = ps
} else {
cat("\n The", length(idxE), "Regions with following IDs are reprocessed for singularity problem: \n")
print(head(as.integer(idxE)))
ssE = summarySeg(seg)[idxE, ]
paraPriorPostError <- setParaPrior(xi = paraPrior$xi, rho = rho2, alpha = paraPrior$alpha, beta = paraPrior$beta,
lambda = paraPrior$lambda, dMu = paraPrior$dMu)
pingE = PING(seg[idxE], paraEM = paraEM, paraPrior = paraPriorPostError, nCores = nCores)
PS1 = as(pingE, "data.frame")
# PS1=as.df(pingE,seg[idxE])
PS1$ID = idxE[PS1$ID]
ps$rank = NULL
PS = rbind(ps, PS1)
# modify rank info to the PING result dataframe
PS = PS[order(PS$score, decreasing = T), ]
PS$rank = 1:nrow(PS)
# if (makePlot) ### make plots {
# pdf(paste(datname,'_rho',rho2,'_DupBound',DupBound,'_pingerror.pdf',sep=''),width=11,height=8.5) for(i in
# 1:nrow(ssE)) { chr=ssE$chr[i]; minbase=ssE$min[i]; maxbase=ssE$max[i] Axis<-makeGenomeAxis(add53 = TRUE, add35 =
# TRUE, littleTicks = TRUE, dp = NULL) title = makeTitle(text =paste(datname, ', ', chr, ':', minbase,'-',maxbase,
# '(',round(maxbase-minbase),'bps), XSET extend ',FragmentLength, ' bps',sep=''), color = 'darkred') XSET.IP =
# makeXSETtrack(IP, chr, m=minbase, M=maxbase, FragmentLength=FragmentLength) Reads.IP =
# new('RawRead',start=unlist(IP[[chr]]), end = unlist(IP[[chr]])+0.1,
# strand=rep(names(IP[[chr]]),lapply(IP[[chr]],length)), dp = DisplayPars(size=4,lwd=3, color=c('red','blue',
# type='l'))) gdPlot(list(title, XSET=XSET.IP,Axis,Reads=Reads.IP), minBase = minbase, maxBase =maxbase) } dev.off()
# pingE.df.f=FilterPING(PS1)$ping.df
# pdf(paste(datname,'_rho',rho2,'_DupBound',DupBound,'_pingEreprocess.pdf',sep=''),width=11,height=8.5) for(i in
# 1:length(pingE)) { plot(pingE[i],seg[idxE[i]]) ff=pingE.df.f$mu[pingE.df.f$chr==seg[[idxE[i]]]@chr]
# abline(v=ff,col=2) } dev.off() }
}
return(PS)
}
######################################################## Usage: Post-process PING results to solve the problem of mismatched peaks (i.e. atypical delta) Input: ping: PING
######################################################## output before post-process seg: PING segmentation results rho: hyper-parameter in prior, which control strengh of
######################################################## prior on 'delta', larger rho means more confidence on prior guess of 'delta' ps: dataframe converted from ping
######################################################## output, which might be already post-processed makePlot: indicator of whether or not make plots of pre- and
######################################################## post-processed PING results in pdf files. Following input parameters is only useful when we need to make plots in
######################################################## pdf files datname: name of datasets, which only used as plot file name DupBound: max # of allowed duplicated reads,
######################################################## which is only used in plot IP: the reads in IP data in 'GenomeData' format FragmentLength: the length of XSET profile
######################################################## extention Output PS: the post-processed PING results used to replace input 'ps'
# PostDelta <- function(ps, ping, seg, rho=8, makePlot=FALSE, datname='', DupBound=NULL, IP=NULL, FragmentLength=100,
# sigmaB2,rho1,alpha1,xi, PE,lambda)
PostDelta <- function(ps, ping, seg, rho2 = 8, makePlot = FALSE, datname = "", DupBound = NULL, IP = NULL, FragmentLength = 100,
paraEM, paraPrior, nCores, sigmaB2, score) {
temp0 = FilterPING(ps, detail = FALSE, deltaB = c(80, 250), sigmaB2 = sigmaB2, sigmaB1 = 10000, seB = Inf, score = score)
# find out who is filtered out by delta
idx = (ps$delta < temp0$myFilter$delta[1]) | (ps$delta > temp0$myFilter$delta[2])
if (sum(idx) == 0) {
print("No predictions with atypical delta")
PS = ps
} else {
ff = ps[idx, ]
ff = ff[order(ff$rank), ]
idxFilt = c(unique(ff$ID))
cat("\n The", length(idxFilt), "Regions with following IDs are reprocessed for atypical delta: \n")
print(head(idxFilt))
paraPriorPostDelta <- setParaPrior(xi = paraPrior$xi, rho = rho2, alpha = paraPrior$alpha, beta = paraPrior$beta,
lambda = paraPrior$lambda, dMu = paraPrior$dMu)
pingFilt = PING(seg[idxFilt], paraEM = paraEM, paraPrior = paraPriorPostDelta, nCores = nCores)
tempPS1 = as(pingFilt, "data.frame")
# tempPS1=as.df(pingFilt,seg[idxFilt])
tempPS1$ID = idxFilt[tempPS1$ID]
tempPS2 = subset(ps, !(ps$ID %in% idxFilt))
tempPS2$rank = NULL
PS = rbind(tempPS2, tempPS1)
PS = PS[order(PS$score, decreasing = T), ]
PS$rank = 1:nrow(PS)
# if(makePlot) { pdf(paste(datname,'_rho',rho2,'_DupBound',DupBound,'_pingFilt_delta.pdf',sep=''),width=11,height=8.5)
# for(i in 1:length(idxFilt)) { plot(ping[idxFilt[i]],seg[idxFilt[i]])
# ff=temp0$ping.df$mu[temp0$ping.df$chr==seg[[idxFilt[i]]]@chr] abline(v=ff,col=2) } dev.off()
# ping.df.f=FilterPING(as(pingFilt,'data.frame'))$ping.df
# pdf(paste(datname,'_rho',rho2,'_DupBound',DupBound,'_pingFilt_delta_Reprocess.pdf',sep=''),width=11,height=8.5) for(i
# in 1:length(idxFilt)) { plot(pingFilt[i],seg[idxFilt[i]]) ff=ping.df.f$mu[ping.df.f$chr==seg[[idxFilt[i]]]@chr]
# abline(v=ff,col=2) } dev.off() }
}
return(PS)
}
######################################################## Usage: Post-process PING results to solve the problem of wrongly merged peaks (i.e. too large sigma) Input: ping:
######################################################## PING output before post-process seg: PING segmentation results ps: dataframe converted from ping output, which might
######################################################## be already post-processed rho: hyper-parameter in prior, which control strengh of prior on 'delta', larger rho means
######################################################## more confidence on prior guess of 'delta' makePlot: indicator of whether or not make plots of pre- and post-processed
######################################################## PING results in pdf files. Following input parameters is only useful when we need to make plots in pdf files
######################################################## datname: name of datasets, which only used as plot file name DupBound: max # of allowed duplicated reads, which is
######################################################## only used in plot IP: the reads in IP data in 'GenomeData' format FragmentLength: the length of XSET profile
######################################################## extention mart: saved gene anotation info obtained from 'ChIPpeakAnno' Output PS: the post-processed PING results
######################################################## used to replace input 'ps' PostSigma <- function(ps, ping, seg, rho=8, makePlot=FALSE, datname='', DupBound=NULL,
######################################################## IP=NULL, FragmentLength=100,mart,sigmaB2,rho1,alpha1,alpha2,beta2,xi,PE,lambda)
PostSigma <- function(ps, ping, seg, rho2 = 8, makePlot = FALSE, datname = "", DupBound = NULL, IP = NULL, FragmentLength = 100,
mart, paraEM, paraPrior, nCores, sigmaB2, alpha2, beta2, score, PE) {
temp = FilterPING(ps, detail = FALSE, deltaB = c(80, 250), sigmaB2 = sigmaB2, sigmaB1 = 10000, seB = Inf, score = score)
# find out who is filtered out by SigmaSq2
idx4 = (ps$sigmaSqF > temp$myFilter$sigmaSq2[2]) & (ps$sigmaSqR > temp$myFilter$sigmaSq2[2])
if (sum(idx4) == 0) {
print("No predictions with atypical sigma")
PS = ps
} else {
ff2 = ps[idx4, ]
ff2 = ff2[order(ff2$rank), ]
idxFiltSigma = ff2$rank
# print('Peaks with following IDs are reprocessed for atypical sigma')
cat("\n The", length(idxFiltSigma), "Peaks with following IDs are reprocessed for atypical sigma: \n")
print(head(idxFiltSigma))
newseg2 = vector("list", length(idxFiltSigma))
for (i in 1:length(idxFiltSigma)) {
newseg2[[i]] = processDup(paras = ps[idxFiltSigma[i], ], seg = seg, nsigma = 2, PE = PE)
}
segSigma = seg
segSigma@List = newseg2
# change hyper-parameters for rho (to avoid atypical delta) and beta (to ask for smaller 'sigma')
paraPriorPostSigma <- setParaPrior(xi = paraPrior$xi, rho = rho2, alpha = alpha2, beta = beta2, lambda = paraPrior$lambda,
dMu = paraPrior$dMu)
system.time(pingSigma <- PING(segSigma, paraEM = paraEM, paraPrior = paraPriorPostSigma, nCores = nCores)) #, PE=PE))
tempPS1 = as(pingSigma, "data.frame")
# tempPS1=as.df(pingSigma,segSigma)
tempPS1$ID = ff2$ID[tempPS1$ID] + 0.2 # I added 0.2 to the ID name to indicate these peaks are post-processed with large sigma
tempPS2 = ps[!idx4, ]
tempPS2$rank = NULL
PS = rbind(tempPS2, tempPS1)
PS = PS[order(PS$score, decreasing = T), ]
PS$rank = 1:nrow(PS)
# if(makePlot) { tmp1=ps tmp1$center=round(tmp1$mu) tmp2=PS tmp2$center=round(tmp2$mu)
# temp$ping.df$center=round(temp$ping.df$mu)
# pdf(paste(datname,'_rho',rho2,'_DupBound',DupBound,'_largeSigma.pdf',sep=''),width=8.5,height=11) for(i in
# 1:nrow(ff2)) { print(paste('plot figure',i,'of', nrow(ff2)))
# try(plotgene(chr=ff2$chr[i],predictions=list(PING_pre=tmp1,PING_post=tmp2), unfilter=list(fAIC3=temp$ping.df),
# unfilter.id=c(1), dif=NULL, datIP=IP, datCtl=NULL, datname=datname, FragmentLength=FragmentLength, genename=NULL,
# genetype='ensembl_gene_id', minbase=ff2$mu[i]-1000, maxbase=ff2$mu[i]+1000,mart=mart, seg=seg) ) } dev.off() }
}
return(PS)
}
######################################################## Usage: Post-process PING results to solve the problem of Duplicated predictions on segment boundaries Input: ping:
######################################################## PING result before post-process
# PostDup <- function(ps, ping, seg, rho=8,rho1,alpha1,xi,PE,min.dist,lambda)
PostDup <- function(ps, ping, seg, rho2 = 8, paraPrior, nCores = nCores, PE, min.dist) {
ps = ps[order(ps$chr, ps$mu), ]
dups = which((diff(ps$ID) != 0) & (diff(ps$mu) < min.dist)) #same ID or center too close to each other
dups = dups[ps$chr[dups] == ps$chr[dups + 1]]
ndup = length(dups)
if (ndup == 0) {
print("No regions with Boudary problems")
PS = ps
} else {
cat("\n The", length(dups), "regions with following IDs are reprocessed for Boundary problems: \n")
print(head(dups))
newseg = vector("list", ndup)
for (i in 1:ndup) {
newseg[[i]] = processDup(paras = ps[dups[i] + c(0, 1), ], seg = seg, PE = PE)
}
segDup = seg
segDup@List = newseg
# paraEM<-setParaEM(minK=1,maxK=15,tol=1e-4,B=100,mSelect='BIC',mergePeaks=TRUE,mapCorrect=TRUE)
paraEM <- setParaEM(minK = 1, maxK = 2, tol = 1e-04, B = 100, mSelect = "AIC3", mergePeaks = TRUE, mapCorrect = TRUE)
paraPriorPostDup <- setParaPrior(xi = paraPrior$xi, rho = rho2, alpha = paraPrior$alpha, beta = paraPrior$beta,
lambda = paraPrior$lambda, dMu = paraPrior$dMu)
system.time(pingDup <- PING(segDup, paraEM = paraEM, paraPrior = paraPriorPostDup, nCores = nCores)) #, PE=PE))
tempPS1 = as(pingDup, "data.frame")
# tempPS1=as.df(pingDup,segDup)
tempPS1$ID = ps[dups[tempPS1$ID], "ID"] + 0.5 # I add 0.5 to indicate these predictions are post-processed duplicated predictions on the boundary of two regions
ps$rank = NULL
PS = rbind(ps[-c(dups, dups + 1), ], tempPS1)
PS = PS[order(PS$score, decreasing = T), ]
PS$rank = 1:nrow(PS)
}
return(PS)
}
######################## Purpose: process duplicated nucs predicted in the overlaped segments for duplicated nucs, I extract the reads in
######################## their F/R peaks, refit the model INPUT: paras: From the data frame converted from PING result, we extract the rows of
######################## possible duplicated nucs predicted cross boundaries of segments. seg: PING segmentation results Output: a segReads
######################## object used to refit PING model
#' @importFrom PICS segReads segReadsPE
processDup <- function(paras, seg, nsigma = 1, PE) {
chr = as.character(paras$chr[1])
muv = paras$mu
deltav = paras$delta
sigmaSqFv = paras$sigmaSqF
sigmaSqRv = paras$sigmaSqR
ID = paras$ID
## find boundaries
sigmaF = sqrt(sigmaSqFv)
sigmaR = sqrt(sigmaSqRv)
startF = min(muv - deltav/2 - nsigma * sigmaF)
endF = max(muv - deltav/2 + nsigma * sigmaF)
startR = min(muv + deltav/2 - nsigma * sigmaR)
endR = max(muv + deltav/2 + nsigma * sigmaR)
# process seg data
IPF = IPR = CTLF = CTLR = numeric(0)
map = matrix(as.integer(0), 0, 2)
for (i in ID) {
temp = seg[[i]]
IPF = c(IPF, temp@yF)
IPR = c(IPR, temp@yR)
CTLF = c(CTLF, temp@cF)
CTLR = c(CTLR, temp@cR)
map = rbind(map, temp@map)
}
IPF = subset(IPF, IPF >= startF)
IPF = subset(IPF, IPF <= endF)
IPR = subset(IPR, IPR >= startR)
IPR = subset(IPR, IPR <= endR)
CTLF = subset(CTLF, CTLF >= startF)
CTLF = subset(CTLF, CTLF <= endF)
CTLR = subset(CTLR, CTLR >= startR)
CTLR = subset(CTLR, CTLR <= endR)
if (PE) {
res = segReadsPE(as.numeric(IPF), as.numeric(IPR), numeric(0), numeric(0), as.numeric(CTLF), as.numeric(CTLR),
numeric(0), numeric(0), map, chr)
} else {
res = segReads(as.numeric(IPF), as.numeric(IPR), as.numeric(CTLF), as.numeric(CTLR), map, chr)
}
}
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Defines functions processDup PostDup PostSigma PostDelta PostError postPING
Documented in postPING
# Usage: Post-process PING results Input: ping: PING result before post-process seg.boundary: a data.frame object gives
# the cutting points of segmentations (cut obtained in segmentation step, not the min/max of reads) if seg.boundary is
# give, all predictions outside of boundary should be removed. This data frame contains 3 columns 'ID' for id of
# candidate regions and 'seg.start'/'seg.end' for start/end points of segment min.dist=100, minimum distance of two
# adjacent nucs, smaller than that will be treated as duplicated prediction on boudary postPING <- function(ping, seg,
# rho=8, makePlot=FALSE, datname='', seg.boundary=NULL, DupBound=NULL, IP=NULL,
# FragmentLength=100,mart=NULL,sigmaB2=2500,rho1=0.8,alpha1=20,alpha2=100,beta2=100000,xi=160, PE=FALSE, min.dist=100,
# lambda=-0.000064) postPING <- function(ping, seg, rho=8,
# sigmaB2=2500,rho1=0.8,alpha1=20,alpha2=100,beta2=100000,xi=150, min.dist=100, lambda=-0.000064)
#' Post process Estimation of binding site positions obtained from PING
#'
#' Post process Estimation of binding site positions obtained from PING. Refit
#' mixture models with stronger prior in candidate regions contain potential
#' problems, and then convert final result into dataframe.
#'
#' @param ping A \code{pingList} object containing estimation of nucleosome
#' positions as returned by the \code{PING} function.
#' @param seg An object of class \code{segmentReadsList} containing the results
#' for all pre-processed regions as returned by \code{segmentReads}.
#' @param paraEM A \code{list} of parameters for the EM algorithm. The default
#' parameters should be good enough for most usages.
#' @param minK An \code{integer}.The minimum number of binding events per region.
#' If the value is 0, the minimum number is automatically calculated.
#' @param maxK An \code{integer}. The maximum number of binding events per region.
#' If the value is 0, the maximum number is automatically calculated.
#' @param tol A \code{numeric}. The tolerance for the EM algorithm.
#' @param B An \code{integer}. The maximum number of iterations to be used.
#' @param mSelect A \code{character} specifying the information criteria to be
#' used when selecting the number of binding events. Default="AIC3"
#' @param mergePeaks A \code{logical} stating whether overlapping binding events should be picked.
#' @param mapCorrect A \code{logical} stating whether mappability profiles should
#' be incorporated in the estimation, i.e: missing reads estimated.
#' @param paraPrior A \code{list} of parameters for the prior distribution. The
#' default parameters should be good enough for most usages.
#' @param xi An \code{integer}. The average DNA fragment size.
#' @param rho An \code{integer}. A variance parameter for the average DNA fragment size distribution.
#' @param alpha An \code{integer}. First hyperparameter of the inverse Gamma
#' distribution for sigma^2 in the PICS model
#' @param beta An \code{integer}. Second hyperparameter of the inverse Gamma
#' distribution for sigma^2 in the PING model
#' @param lambda An \code{integer}. The lambda control Gaussian Markov Random
#' Field prior on the distance of adjacent nucleosomes, we do not recommend user
#' change the default value.
#' @param dMu An \code{integer}. Our best guess for the distance between two
#' neighboring nucleosomes.
#' @param rho2,sigmaB2,alpha2,beta2 Integer values, the parameters in the
#' prior of mixture models to be re-fitted.
#' @param min.dist The minimum distance of two adjacent nucleosomes predicted
#' from different candidate regions, smaller than that will be treated as
#' duplicated predictions for the same nucleosomes.
#' @param score A \code{numeric}. The score threshold used when calling \code{FilterPING}.
#' @param dataType A \code{character} that can be set to use selected default
#' parameters for the algorithm.
#' @param nCores An \code{integer}. The number of cores that should be used in
#' parallel by the function.
#' @param makePlot A \code{logical}. Plot a summary of the output.
#' @param mart,seg.boundary,DupBound,datname Plotting parameters and options.
#' @param IP A \code{GRanges} object. The reads used in segmentation process.
#' @param FragmentLength An \code{integer}. The length of XSET profile extension
#'
#' @note
#' Based on our experiemt on a few real data sets, we suggestion to use following
#' values of parameters. For sonication data we use rho1=1.2; sigmaB2=6400;
#' rho=15; alpha1=10; alpha2=98; beta2=200000. For MNase data we use rho1=3;
#' sigmaB2=4900; rho=8; alpha1=20; alpha2=100; beta2=100000. The value of xi
#' depends on specs of sample, since that affect the length of linker-DNA.
#' For example, we use xi=160 for yeast and xi=200 for mouse.
#'
#' @return A \code{data.frame} containing the estimated binding site positions
#'
#' @seealso PING, plotSummary
#'
#' @importFrom PICS setParaEM setParaPrior
#' @export
postPING <- function(ping, seg, rho2 = NULL, sigmaB2 = NULL, alpha2 = NULL,
beta2 = NULL, min.dist = 100, paraEM = NULL,
paraPrior = NULL, score = 0.05, dataType = "MNase",
nCores = 1, makePlot = FALSE, FragmentLength = 100,
mart = NULL, seg.boundary = NULL, DupBound = NULL,
IP = NULL, datname = "") {
if (length(ping) != length(seg)) {
stop("The length of `ping' and `seg' arguments are different. `seg' must be the same used when calling PING.")
}
PE <- ping@PE
if (length(paraPrior) != 6) {
if (isTRUE(PE))
paraPrior <- setParaPrior(dataType = dataType, PExi = seg@paraSW$xi) else paraPrior <- setParaPrior(dataType = dataType)
}
if (length(paraEM) != 7) {
paraEM <- setParaEM(dataType = dataType)
}
if (length(c(rho2, sigmaB2, alpha2, beta2)) != 4 | !is.numeric(c(rho2, sigmaB2, alpha2, beta2))) {
if (tolower(dataType) == "mnase") {
message("Using default refitting parameters for MNase data, for sonicated data, set the argument dataType")
rho2 <- 8
sigmaB2 <- 4900
alpha2 <- 100
beta2 <- 1e+05
} else if (tolower(dataType) == "sonicated") {
message("Using default refitting parameters for sonicated data")
rho2 <- 15
sigmaB2 <- 6400
alpha2 <- 98
beta2 <- 2e+05
} else {
stop("Invalid dataType, must be either 'MNase' or 'sonicated'")
}
}
# 'Sonication': {rho1=1.2; sigmaB2=6400;rho=15;alpha1=10; alpha2=98; beta2=200000} MNase: {rho1=3; sigmaB2=4900; rho=8;
# alpha1=20; alpha2=100; beta2=100000} produce the PING result dataframe and add rank info
ps = as(ping, "data.frame")
# ps=as.df(ping,seg)
if (!is.null(seg.boundary)) {
temp <- merge(ps, seg.boundary, all.x = T, all.y = FALSE, by = "ID")
idx <- ((temp$mu >= temp$seg.start) & (temp$mu <= temp$seg.end))
ps <- ps[idx, ]
}
ps = ps[order(ps$score, decreasing = T), ]
ps$rank = 1:nrow(ps)
ps1 = PostError(ps = ps, ping = ping, seg = seg, makePlot = makePlot, datname = datname, DupBound = DupBound, IP = IP,
FragmentLength = FragmentLength, paraEM = paraEM, paraPrior = paraPrior, nCores = nCores, rho2 = rho2)
ps2 = PostDelta(ps = ps1, ping = ping, seg = seg, makePlot = makePlot, datname = datname, DupBound = DupBound, IP = IP,
FragmentLength = FragmentLength, paraEM = paraEM, paraPrior = paraPrior, nCores = nCores, rho2 = rho2, sigmaB2 = sigmaB2,
score = score)
ps3 = PostSigma(ps = ps2, ping = ping, seg = seg, rho2 = rho2, makePlot = makePlot, datname = datname, DupBound = DupBound,
IP = IP, FragmentLength = FragmentLength, mart = mart, sigmaB2 = sigmaB2, paraEM = paraEM, paraPrior = paraPrior,
nCores = nCores, alpha2 = alpha2, beta2 = beta2, score = score, PE = PE)
PS = PostDup(ps = ps3, ping = ping, seg = seg, rho2 = rho2, paraPrior = paraPrior, nCores = nCores, PE = PE, min.dist = min.dist)
return(PS)
}
######################################################## Usage: Post-process PING results to solve the singularity problem of PING model fitting Input: ping: PING output
######################################################## before post-process seg: PING segmentation results rho: hyper-parameter in prior, which control strengh of prior on
######################################################## 'delta', larger rho means more confidence on prior guess of 'delta' ps: dataframe converted from ping output, which
######################################################## might be already post-processed makePlot: indicator of whether or not make plots of pre- and post-processed PING
######################################################## results in pdf files. Following input parameters is only useful when we need to make plots in pdf files datname:
######################################################## name of datasets, which only used as plot file name DupBound: max # of allowed duplicated reads, which is only used
######################################################## in plot IP: the reads in IP data in 'GenomeData' format FragmentLength: the length of XSET profile extention Output
######################################################## PS: the post-processed PING results used to replace input 'ps' PostError <- function(ps, ping, seg, rho=8,
######################################################## makePlot=FALSE, datname='', DupBound=NULL, IP=NULL, FragmentLength=100,rho1,alpha1,xi, PE,lambda)
#' @importFrom PICS code
PostError <- function(ps, ping, seg, rho2 = 8, makePlot = FALSE, datname = "", DupBound = NULL, IP = NULL, FragmentLength = 100,
paraEM, paraPrior, nCores) {
idxE = which(code(ping) != "")
if (length(idxE) == 0) {
print("No regions with pingerror")
PS = ps
} else {
cat("\n The", length(idxE), "Regions with following IDs are reprocessed for singularity problem: \n")
print(head(as.integer(idxE)))
ssE = summarySeg(seg)[idxE, ]
paraPriorPostError <- setParaPrior(xi = paraPrior$xi, rho = rho2, alpha = paraPrior$alpha, beta = paraPrior$beta,
lambda = paraPrior$lambda, dMu = paraPrior$dMu)
pingE = PING(seg[idxE], paraEM = paraEM, paraPrior = paraPriorPostError, nCores = nCores)
PS1 = as(pingE, "data.frame")
# PS1=as.df(pingE,seg[idxE])
PS1$ID = idxE[PS1$ID]
ps$rank = NULL
PS = rbind(ps, PS1)
# modify rank info to the PING result dataframe
PS = PS[order(PS$score, decreasing = T), ]
PS$rank = 1:nrow(PS)
# if (makePlot) ### make plots {
# pdf(paste(datname,'_rho',rho2,'_DupBound',DupBound,'_pingerror.pdf',sep=''),width=11,height=8.5) for(i in
# 1:nrow(ssE)) { chr=ssE$chr[i]; minbase=ssE$min[i]; maxbase=ssE$max[i] Axis<-makeGenomeAxis(add53 = TRUE, add35 =
# TRUE, littleTicks = TRUE, dp = NULL) title = makeTitle(text =paste(datname, ', ', chr, ':', minbase,'-',maxbase,
# '(',round(maxbase-minbase),'bps), XSET extend ',FragmentLength, ' bps',sep=''), color = 'darkred') XSET.IP =
# makeXSETtrack(IP, chr, m=minbase, M=maxbase, FragmentLength=FragmentLength) Reads.IP =
# new('RawRead',start=unlist(IP[[chr]]), end = unlist(IP[[chr]])+0.1,
# strand=rep(names(IP[[chr]]),lapply(IP[[chr]],length)), dp = DisplayPars(size=4,lwd=3, color=c('red','blue',
# type='l'))) gdPlot(list(title, XSET=XSET.IP,Axis,Reads=Reads.IP), minBase = minbase, maxBase =maxbase) } dev.off()
# pingE.df.f=FilterPING(PS1)$ping.df
# pdf(paste(datname,'_rho',rho2,'_DupBound',DupBound,'_pingEreprocess.pdf',sep=''),width=11,height=8.5) for(i in
# 1:length(pingE)) { plot(pingE[i],seg[idxE[i]]) ff=pingE.df.f$mu[pingE.df.f$chr==seg[[idxE[i]]]@chr]
# abline(v=ff,col=2) } dev.off() }
}
return(PS)
}
######################################################## Usage: Post-process PING results to solve the problem of mismatched peaks (i.e. atypical delta) Input: ping: PING
######################################################## output before post-process seg: PING segmentation results rho: hyper-parameter in prior, which control strengh of
######################################################## prior on 'delta', larger rho means more confidence on prior guess of 'delta' ps: dataframe converted from ping
######################################################## output, which might be already post-processed makePlot: indicator of whether or not make plots of pre- and
######################################################## post-processed PING results in pdf files. Following input parameters is only useful when we need to make plots in
######################################################## pdf files datname: name of datasets, which only used as plot file name DupBound: max # of allowed duplicated reads,
######################################################## which is only used in plot IP: the reads in IP data in 'GenomeData' format FragmentLength: the length of XSET profile
######################################################## extention Output PS: the post-processed PING results used to replace input 'ps'
# PostDelta <- function(ps, ping, seg, rho=8, makePlot=FALSE, datname='', DupBound=NULL, IP=NULL, FragmentLength=100,
# sigmaB2,rho1,alpha1,xi, PE,lambda)
PostDelta <- function(ps, ping, seg, rho2 = 8, makePlot = FALSE, datname = "", DupBound = NULL, IP = NULL, FragmentLength = 100,
paraEM, paraPrior, nCores, sigmaB2, score) {
temp0 = FilterPING(ps, detail = FALSE, deltaB = c(80, 250), sigmaB2 = sigmaB2, sigmaB1 = 10000, seB = Inf, score = score)
# find out who is filtered out by delta
idx = (ps$delta < temp0$myFilter$delta[1]) | (ps$delta > temp0$myFilter$delta[2])
if (sum(idx) == 0) {
print("No predictions with atypical delta")
PS = ps
} else {
ff = ps[idx, ]
ff = ff[order(ff$rank), ]
idxFilt = c(unique(ff$ID))
cat("\n The", length(idxFilt), "Regions with following IDs are reprocessed for atypical delta: \n")
print(head(idxFilt))
paraPriorPostDelta <- setParaPrior(xi = paraPrior$xi, rho = rho2, alpha = paraPrior$alpha, beta = paraPrior$beta,
lambda = paraPrior$lambda, dMu = paraPrior$dMu)
pingFilt = PING(seg[idxFilt], paraEM = paraEM, paraPrior = paraPriorPostDelta, nCores = nCores)
tempPS1 = as(pingFilt, "data.frame")
# tempPS1=as.df(pingFilt,seg[idxFilt])
tempPS1$ID = idxFilt[tempPS1$ID]
tempPS2 = subset(ps, !(ps$ID %in% idxFilt))
tempPS2$rank = NULL
PS = rbind(tempPS2, tempPS1)
PS = PS[order(PS$score, decreasing = T), ]
PS$rank = 1:nrow(PS)
# if(makePlot) { pdf(paste(datname,'_rho',rho2,'_DupBound',DupBound,'_pingFilt_delta.pdf',sep=''),width=11,height=8.5)
# for(i in 1:length(idxFilt)) { plot(ping[idxFilt[i]],seg[idxFilt[i]])
# ff=temp0$ping.df$mu[temp0$ping.df$chr==seg[[idxFilt[i]]]@chr] abline(v=ff,col=2) } dev.off()
# ping.df.f=FilterPING(as(pingFilt,'data.frame'))$ping.df
# pdf(paste(datname,'_rho',rho2,'_DupBound',DupBound,'_pingFilt_delta_Reprocess.pdf',sep=''),width=11,height=8.5) for(i
# in 1:length(idxFilt)) { plot(pingFilt[i],seg[idxFilt[i]]) ff=ping.df.f$mu[ping.df.f$chr==seg[[idxFilt[i]]]@chr]
# abline(v=ff,col=2) } dev.off() }
}
return(PS)
}
######################################################## Usage: Post-process PING results to solve the problem of wrongly merged peaks (i.e. too large sigma) Input: ping:
######################################################## PING output before post-process seg: PING segmentation results ps: dataframe converted from ping output, which might
######################################################## be already post-processed rho: hyper-parameter in prior, which control strengh of prior on 'delta', larger rho means
######################################################## more confidence on prior guess of 'delta' makePlot: indicator of whether or not make plots of pre- and post-processed
######################################################## PING results in pdf files. Following input parameters is only useful when we need to make plots in pdf files
######################################################## datname: name of datasets, which only used as plot file name DupBound: max # of allowed duplicated reads, which is
######################################################## only used in plot IP: the reads in IP data in 'GenomeData' format FragmentLength: the length of XSET profile
######################################################## extention mart: saved gene anotation info obtained from 'ChIPpeakAnno' Output PS: the post-processed PING results
######################################################## used to replace input 'ps' PostSigma <- function(ps, ping, seg, rho=8, makePlot=FALSE, datname='', DupBound=NULL,
######################################################## IP=NULL, FragmentLength=100,mart,sigmaB2,rho1,alpha1,alpha2,beta2,xi,PE,lambda)
PostSigma <- function(ps, ping, seg, rho2 = 8, makePlot = FALSE, datname = "", DupBound = NULL, IP = NULL, FragmentLength = 100,
mart, paraEM, paraPrior, nCores, sigmaB2, alpha2, beta2, score, PE) {
temp = FilterPING(ps, detail = FALSE, deltaB = c(80, 250), sigmaB2 = sigmaB2, sigmaB1 = 10000, seB = Inf, score = score)
# find out who is filtered out by SigmaSq2
idx4 = (ps$sigmaSqF > temp$myFilter$sigmaSq2[2]) & (ps$sigmaSqR > temp$myFilter$sigmaSq2[2])
if (sum(idx4) == 0) {
print("No predictions with atypical sigma")
PS = ps
} else {
ff2 = ps[idx4, ]
ff2 = ff2[order(ff2$rank), ]
idxFiltSigma = ff2$rank
# print('Peaks with following IDs are reprocessed for atypical sigma')
cat("\n The", length(idxFiltSigma), "Peaks with following IDs are reprocessed for atypical sigma: \n")
print(head(idxFiltSigma))
newseg2 = vector("list", length(idxFiltSigma))
for (i in 1:length(idxFiltSigma)) {
newseg2[[i]] = processDup(paras = ps[idxFiltSigma[i], ], seg = seg, nsigma = 2, PE = PE)
}
segSigma = seg
segSigma@List = newseg2
# change hyper-parameters for rho (to avoid atypical delta) and beta (to ask for smaller 'sigma')
paraPriorPostSigma <- setParaPrior(xi = paraPrior$xi, rho = rho2, alpha = alpha2, beta = beta2, lambda = paraPrior$lambda,
dMu = paraPrior$dMu)
system.time(pingSigma <- PING(segSigma, paraEM = paraEM, paraPrior = paraPriorPostSigma, nCores = nCores)) #, PE=PE))
tempPS1 = as(pingSigma, "data.frame")
# tempPS1=as.df(pingSigma,segSigma)
tempPS1$ID = ff2$ID[tempPS1$ID] + 0.2 # I added 0.2 to the ID name to indicate these peaks are post-processed with large sigma
tempPS2 = ps[!idx4, ]
tempPS2$rank = NULL
PS = rbind(tempPS2, tempPS1)
PS = PS[order(PS$score, decreasing = T), ]
PS$rank = 1:nrow(PS)
# if(makePlot) { tmp1=ps tmp1$center=round(tmp1$mu) tmp2=PS tmp2$center=round(tmp2$mu)
# temp$ping.df$center=round(temp$ping.df$mu)
# pdf(paste(datname,'_rho',rho2,'_DupBound',DupBound,'_largeSigma.pdf',sep=''),width=8.5,height=11) for(i in
# 1:nrow(ff2)) { print(paste('plot figure',i,'of', nrow(ff2)))
# try(plotgene(chr=ff2$chr[i],predictions=list(PING_pre=tmp1,PING_post=tmp2), unfilter=list(fAIC3=temp$ping.df),
# unfilter.id=c(1), dif=NULL, datIP=IP, datCtl=NULL, datname=datname, FragmentLength=FragmentLength, genename=NULL,
# genetype='ensembl_gene_id', minbase=ff2$mu[i]-1000, maxbase=ff2$mu[i]+1000,mart=mart, seg=seg) ) } dev.off() }
}
return(PS)
}
######################################################## Usage: Post-process PING results to solve the problem of Duplicated predictions on segment boundaries Input: ping:
######################################################## PING result before post-process
# PostDup <- function(ps, ping, seg, rho=8,rho1,alpha1,xi,PE,min.dist,lambda)
PostDup <- function(ps, ping, seg, rho2 = 8, paraPrior, nCores = nCores, PE, min.dist) {
ps = ps[order(ps$chr, ps$mu), ]
dups = which((diff(ps$ID) != 0) & (diff(ps$mu) < min.dist)) #same ID or center too close to each other
dups = dups[ps$chr[dups] == ps$chr[dups + 1]]
ndup = length(dups)
if (ndup == 0) {
print("No regions with Boudary problems")
PS = ps
} else {
cat("\n The", length(dups), "regions with following IDs are reprocessed for Boundary problems: \n")
print(head(dups))
newseg = vector("list", ndup)
for (i in 1:ndup) {
newseg[[i]] = processDup(paras = ps[dups[i] + c(0, 1), ], seg = seg, PE = PE)
}
segDup = seg
segDup@List = newseg
# paraEM<-setParaEM(minK=1,maxK=15,tol=1e-4,B=100,mSelect='BIC',mergePeaks=TRUE,mapCorrect=TRUE)
paraEM <- setParaEM(minK = 1, maxK = 2, tol = 1e-04, B = 100, mSelect = "AIC3", mergePeaks = TRUE, mapCorrect = TRUE)
paraPriorPostDup <- setParaPrior(xi = paraPrior$xi, rho = rho2, alpha = paraPrior$alpha, beta = paraPrior$beta,
lambda = paraPrior$lambda, dMu = paraPrior$dMu)
system.time(pingDup <- PING(segDup, paraEM = paraEM, paraPrior = paraPriorPostDup, nCores = nCores)) #, PE=PE))
tempPS1 = as(pingDup, "data.frame")
# tempPS1=as.df(pingDup,segDup)
tempPS1$ID = ps[dups[tempPS1$ID], "ID"] + 0.5 # I add 0.5 to indicate these predictions are post-processed duplicated predictions on the boundary of two regions
ps$rank = NULL
PS = rbind(ps[-c(dups, dups + 1), ], tempPS1)
PS = PS[order(PS$score, decreasing = T), ]
PS$rank = 1:nrow(PS)
}
return(PS)
}
######################## Purpose: process duplicated nucs predicted in the overlaped segments for duplicated nucs, I extract the reads in
######################## their F/R peaks, refit the model INPUT: paras: From the data frame converted from PING result, we extract the rows of
######################## possible duplicated nucs predicted cross boundaries of segments. seg: PING segmentation results Output: a segReads
######################## object used to refit PING model
#' @importFrom PICS segReads segReadsPE
processDup <- function(paras, seg, nsigma = 1, PE) {
chr = as.character(paras$chr[1])
muv = paras$mu
deltav = paras$delta
sigmaSqFv = paras$sigmaSqF
sigmaSqRv = paras$sigmaSqR
ID = paras$ID
## find boundaries
sigmaF = sqrt(sigmaSqFv)
sigmaR = sqrt(sigmaSqRv)
startF = min(muv - deltav/2 - nsigma * sigmaF)
endF = max(muv - deltav/2 + nsigma * sigmaF)
startR = min(muv + deltav/2 - nsigma * sigmaR)
endR = max(muv + deltav/2 + nsigma * sigmaR)
# process seg data
IPF = IPR = CTLF = CTLR = numeric(0)
map = matrix(as.integer(0), 0, 2)
for (i in ID) {
temp = seg[[i]]
IPF = c(IPF, temp@yF)
IPR = c(IPR, temp@yR)
CTLF = c(CTLF, temp@cF)
CTLR = c(CTLR, temp@cR)
map = rbind(map, temp@map)
}
IPF = subset(IPF, IPF >= startF)
IPF = subset(IPF, IPF <= endF)
IPR = subset(IPR, IPR >= startR)
IPR = subset(IPR, IPR <= endR)
CTLF = subset(CTLF, CTLF >= startF)
CTLF = subset(CTLF, CTLF <= endF)
CTLR = subset(CTLR, CTLR >= startR)
CTLR = subset(CTLR, CTLR <= endR)
if (PE) {
res = segReadsPE(as.numeric(IPF), as.numeric(IPR), numeric(0), numeric(0), as.numeric(CTLF), as.numeric(CTLR),
numeric(0), numeric(0), map, chr)
} else {
res = segReads(as.numeric(IPF), as.numeric(IPR), as.numeric(CTLF), as.numeric(CTLR), map, chr)
}
}
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