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dmrcate.R
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dmrcate.R
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dmrcate <-
function (object,
lambda = 1000,
C = NULL,
pcutoff = "fdr",
consec = FALSE,
conseclambda = 10,
betacutoff = NULL,
min.cpgs = 2
)
{
## Arguments
stopifnot(is(object, "CpGannotated"))
stopifnot(lambda >= 1)
stopifnot(pcutoff == "fdr" | (0 <= pcutoff & pcutoff <= 1))
stopifnot(C >= 0.2)
if (consec & is.null(conseclambda)) {
stop("Consecutive CpG bandwidth must be specified")
}
## Modified 'object'
object <-
data.frame(ID = names(object@ranges),
weights = abs(object@ranges$stat),
CHR = seqnames(object@ranges),
pos = start(object@ranges),
rawpval = object@ranges$rawpval,
diff = object@ranges$diff,
indfdr = object@ranges$ind.fdr,
is.sig = object@ranges$is.sig
)
# Order by position
object <- object[order(object$CHR, object$pos),]
# Remove any chromosome with exactly 1 probe
if (any(table(object$CHR)==1)) {
torm <- names(which(table(object$CHR)==1))
object <- object[!object$CHR %in% torm,]
}
# Automatic bandwidth specification
if (is.null(C) & !consec) {
C = 2
}
## Handle 'consec' case
if (consec)
{
lambda = conseclambda
message(paste("Consecutive mode specified, lambda is now set at", conseclambda, "consecutive CpGs."))
if (is.null(C)){
stop("Error: argument C must be specified (in CpG sites) for consecutive mode.")
}
object$realcoordforconsec <- object$pos
object$pos <- unlist(sapply(as.numeric(table(object$CHR)), function (x) 1:x))
}
## Kernel (chi-squared) test via 'fitParallel'
lag = lambda
chr.unique <- unique(c(as.character(object$CHR)))
fitted <-
lapply(chr.unique,
fitParallel,
object = object,
consec = consec,
conseclambda = conseclambda,
lambda = lambda,
C = C
)
object <- rbind.fill(fitted)
## FDR stuff
object$fdr <- p.adjust(object$raw, method = "BH")
if (pcutoff == "fdr")
{
nsig <- sum(object$is.sig)
if (nsig == 0)
{
txt <- "The FDR you specified in cpg.annotate() returned no significant CpGs, hence there are no DMRs.\n Try specifying a value of 'pcutoff' in dmrcate() and/or increasing 'fdr' in cpg.annotate()."
stop(paste(strwrap(txt, exdent = 2), collapse = "\n"))
}
pcutoff <- sort(object$fdr)[nsig]
}
object$sig <- (object$fdr <= pcutoff)
if (nrow(object) == 0)
{
txt <- "No signficant regions found. Try increasing the value of\n 'pcutoff' in dmrcate() and/or 'fdr' in cpg.annotate()."
stop(paste(strwrap(txt, exdent = 2), collapse = "\n"))
}
## Segmentation
message("Demarcating regions...")
# Define jump.k
# K = number of significant CpGs
# k = K - 1
chr.N <- as.character(object$CHR)
pos.N <- object$pos
sig.N <- object$sig
N <- length(sig.N)
n.K <- which(sig.N)
K <- length(n.K)
stopifnot(K >= 2)
pos.K <- pos.N[n.K]
chr.K <- chr.N[n.K]
jump_chr.k <- (chr.K[-1] != chr.K[-K])
jump_pos.k <- (diff(pos.K) > lag)
jump.k <- (jump_chr.k | jump_pos.k)
# Segment using jump.k
ksegments.A2 <- Segment(jump.k)
A <- nrow(ksegments.A2)
# Extract start/end indices
kstart.A <- ksegments.A2[,"start"]
kend.A <- ksegments.A2[,"end"]
## Regionwise stats
# Positions
realpos.K <- pos.K
if(consec)
{
realpos.N <- object$realcoordforconsec
realpos.K <- realpos.N[n.K]
}
# Per-DMR: Coordinates
start.A <- realpos.K[kstart.A]
end.A <- realpos.K[kend.A]
chr.A <- chr.K[kstart.A]
stopifnot(all(chr.K[kend.A] == chr.A))
fmt <- "%s:%1d-%1d"
coord.A <- sprintf(fmt, chr.A, start.A, end.A)
# Region factor
nstart.A <- n.K[kstart.A]
nend.A <- n.K[kend.A]
width.A <- nend.A + 1 - nstart.A
a.Z <- rep(seq(A), width.A) # a.Z
fn <-
function(a)
seq(from = nstart.A[a], to = nend.A[a])
l.listA <- lapply(seq(A), fn)
n.Z <- unlist(l.listA)
region.N <- rep(NA_integer_, N)
region.N[n.Z] <- a.Z
levels <- seq(A)
region.N <- factor(region.N, levels = levels)
# Per-DMR: Number of CpGs
no_cpg.A <- c(table(region.N))
# Function to do regionwise summaries
REGIONSTAT <-
function(field,
fn
)
{
x.N <- object[[field]]
x.R <- tapply(x.N, region.N, fn)
c(x.R)
}
# results <- region-wise stats
fn_Stouffer <- function(x) pnorm(sum(qnorm(x))/sqrt(length(x)))
fn_HMpval <- function (x) 1/mean(1/x)
fn_Fisher <- function (x) pchisq((sum(log(x))*-2), df=length(x)*2, lower.tail=FALSE)
fn_max <- function(x) x[which.max(abs(x))]
results <-
data.frame(
coord = coord.A,
no.cpgs = no_cpg.A,
min_smoothed_fdr = REGIONSTAT("fdr", min),
Stouffer = REGIONSTAT("rawpval", fn_Stouffer),
HMpval = REGIONSTAT("rawpval", fn_HMpval),
Fisher = REGIONSTAT("rawpval", fn_Fisher),
maxdiff = REGIONSTAT("diff", fn_max),
meandiff = REGIONSTAT("diff", mean),
row.names = seq(A),
stringsAsFactors = FALSE
)
#Correct DMR-wise "significances"
results$Stouffer <- p.adjust(results$Stouffer, method = "fdr")
results$Fisher <- p.adjust(results$Fisher, method = "fdr")
results$HMFDR <- p.adjust(results$HMpval, method = "fdr")
# Order and filter DMRs
keep <- (results$no.cpgs >= min.cpgs)
results <- results[keep, ]
if(!(is.null(betacutoff))){
message("Warning: betacutoff only meaningful for Illumina array data or WGBS results from DSS::DMLtest().")
keep <- (abs(results$meandiff) > betacutoff)
results <- results[keep, ]
}
o <- order(results$min_smoothed_fdr, -results$no.cpgs)
results <- results[o,]
message("Done!")
return(new("DMResults", coord=results$coord, no.cpgs=results$no.cpgs, min_smoothed_fdr=results$min_smoothed_fdr,
Stouffer=results$Stouffer, HMFDR=results$HMFDR, Fisher=results$Fisher, maxdiff=results$maxdiff, meandiff=results$meandiff))
}