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functions.R
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functions.R
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prejoin <- function(dt, ext=250, width=NULL){
if(is.null(width)){ # extend CI ends by fixed amount
dt[,CI_start_ext := CI_start -ext]
dt[,CI_stop_ext := CI_stop +ext]
}else{ # set total peak width as set value around center
dt[,CI_start_ext := center_start - width/2]
dt[,CI_stop_ext := center_stop + width/2]
}
setkey(dt, chr, CI_start_ext, CI_stop_ext)
return(dt)
}
trim_peaks <- function(dt, max_len=1000){
dt[,width := CI_stop-CI_start]
dt[,CI_start_ext := as.integer(CI_start_ext)]
dt[,CI_stop_ext := as.integer(CI_stop_ext)]
dt[,CI_start_ext := as.integer(CI_start + max(0,(width/2)-(max_len/2))), by=c("chr", "CI_start", "CI_stop")]
dt[,CI_stop_ext := as.integer(CI_stop - max(0,(width/2)-(max_len/2))), by=c("chr", "CI_start", "CI_stop")]
setkey(dt, chr, CI_start_ext, CI_stop_ext)
return(dt)
}
fraction_overlapN_old <- function(dt,x,y,n=100){
setorder(dt, enrichment)
binning_vector <- cut(1:nrow(dt), n)
plot(1:n/n, tapply(!is.na(dt[,get(y)]), binning_vector, mean),
xlab=paste("Fraction of",x,"Peaks (ordered low to high enrichment)"),
ylab=paste("Fraction of",x,"peaks that overlap",y,"peaks"))
}
fraction_overlapN <- function(dt,x,y, n=25, filters=c("All"), returndf=F){
setorder(dt, enrichment)
if(is.integer(dt$enrichment)){
dt$enrichment_bin <- dt$enrichment
warning("Using enrichment as bin (integer type detected)")
}else{
dt$enrichment_bin <- cut(1:nrow(dt), n)
}
All=TRUE
tmp <- dt[eval(parse(text=filters[1])),.(mean_enrichment=mean(enrichment),
num=.N,
Overlap=mean(!is.na(get(y))),
Subset=filters[1],
#sem=sd(!is.na(get(y)))/sqrt(length(get(y))),
sep=sqrt((mean(!is.na(get(y))) * (1- mean(!is.na(get(y)))))/length(get(y)))),by=enrichment_bin]
#dt[,mean(!is.na(get(y)))]
if(returndf){
return(tmp)
}else{
return(
ggplot(tmp, aes(mean_enrichment, Overlap, colour=Subset, group=Subset)) +
#geom_point(size=2) +
geom_hline(yintercept = dt[,mean(!is.na(get(y)))], colour="blue", linetype="dashed") +
geom_pointrange(aes(ymax = Overlap + 2*sep, ymin = Overlap - 2*sep)) +
theme_minimal() +
scale_color_brewer(palette = 'Set1') +
xlab(paste("Mean",x,"Enrichment")) +
scale_x_log10() +
ylab(paste("Fraction of ",x,"peaks\n that overlap",y,"peaks"))
)}
}
randomise_positions <- function(base, shift){
base_chr_lengths <- base[,.("chr_len"=max(CI_stop_ext)),by=chr]
setkey(base_chr_lengths, chr)
base_shifted <- base[base_chr_lengths, on="chr"]
base_shifted[,max_right_shift := min(chr_len,CI_stop_ext+shift) - CI_stop_ext, by=c("chr", "CI_start_ext", "CI_stop_ext")]
base_shifted[,max_left_shift := CI_start_ext - max(0,CI_start_ext-shift), by=c("chr", "CI_start_ext", "CI_stop_ext")]
set.seed(42)
#shifts <- sample(-shift:shift, nrow(base_shifted), replace = T)
base_shifted[,shift := sample(-max_left_shift:max_right_shift,1), by=c("chr", "CI_start_ext", "CI_stop_ext")]
base_shifted[,CI_start_ext := CI_start_ext + shift]
base_shifted[,CI_stop_ext := CI_stop_ext + shift]
setkey(base_shifted, chr, CI_start_ext, CI_stop_ext)
return(base_shifted)
}
fraction_overlapN2 <- function(x,y, x1, y1, n=25, shift=1e5, filters=c("All"), returndf=F, corrected=F){
base <- x[,.(chr, CI_start_ext, CI_stop_ext, enrichment)]
test <- y[,.(chr, CI_start_ext, CI_stop_ext)] # enrichment
setkey(base, chr, CI_start_ext, CI_stop_ext)
setkey(test, chr, CI_start_ext, CI_stop_ext)
base_shifted <- randomise_positions(base, shift)
base$test_enrichment <- foverlaps(base, test, mult="first")$CI_start_ext # enrichment
base_shifted$test_enrichment <- foverlaps(base_shifted, test, mult="first")$CI_start_ext # enrichment
a <- fraction_overlapN(base, "base", "test_enrichment", n=n, returndf = T)
b <- fraction_overlapN(base_shifted, "base_shifted", "test_enrichment",n=n, returndf = T)
a$Type <- "Observed"
b$Type <- "Randomised"
tmp <- rbind(a,b)
if(corrected){
tmp <- dcast(tmp, enrichment_bin + mean_enrichment + num + Subset ~ Type, value.var = "Overlap")
tmp[,Overlap := (1 - ( (1-Observed) / (1-Randomised) ))]
tmp[,Type := "Corrected"]
tmp[,sep := sqrt((Overlap * (1- Overlap))/num), by=enrichment_bin]
}
if(returndf){
return(tmp)
}else{
p <- ggplot(tmp, aes(mean_enrichment, Overlap, colour=Type, group=Type))
if(!corrected){
p <- p + geom_hline(yintercept = base[,mean(!is.na(test_enrichment))], colour="#E41A1C", linetype="dashed") +
geom_hline(yintercept = base_shifted[,mean(!is.na(test_enrichment))], colour="#377EB8", linetype="dashed")
}
return(p +
geom_pointrange(aes(ymax = Overlap + 2*sep, ymin = Overlap - 2*sep)) +
theme_minimal() +
scale_color_brewer(palette = 'Set1') +
xlab(paste("Mean",x1,"Enrichment")) +
scale_x_log10() +
ylim(-0.01,1.01) +
ylab(paste("Fraction of ",x1,"peaks\n that overlap",y1,"peaks"))
)}
}
fraction_overlapP <- function(dt,x,y,n=100){
setorder(dt, -pvalue)
binning_vector <- cut(1:nrow(dt), n)
plot(1:n/n, tapply(!is.na(dt[,get(y)]), binning_vector, mean),
xlab=paste("Fraction of",x,"Peaks (ordered large to small pvalue)"),
ylab=paste("Fraction of",x,"peaks that overlap",y,"peaks"))
}
loadBed <- function(file, ext=250){
Trim28 <- fread(file)
names(Trim28)[1:3] <- c("chr","CI_start","CI_stop")
Trim28 <- prejoin(Trim28, ext)
return(Trim28)
}
overlapGam <- function(x, y, shift=NULL, range=c(0.01,50), returngam=F){
base <- x[,.(chr, CI_start_ext, CI_stop_ext, enrichment)]
test <- y[,.(chr, CI_start_ext, CI_stop_ext)] # enrichment
setkey(base, chr, CI_start_ext, CI_stop_ext)
setkey(test, chr, CI_start_ext, CI_stop_ext)
if(!is.null(shift)){
base <- randomise_positions(base, shift)
}
base$test_enrichment <- foverlaps(base, test, mult="first")$CI_start_ext # enrichment
base$overlap <- !is.na(base$test_enrichment)
gam_fit <- gam(data=base, overlap ~ s(enrichment), family="quasibinomial")
if(returngam){
return(gam_fit)
}else{
n=500
x_new <- seq(range[1], range[2], length.out = n)
gam_pred <- data.table(enrichment = x_new,
data.frame(predict(gam_fit, data.frame(enrichment = x_new), se.fit=TRUE, type="response")))
gam_pred <- cbind(gam_pred, Type="GAM")
setnames(gam_pred, c("mean_enrichment","Overlap","se","Type"))
return(gam_pred)
}
}