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useful_functions.R
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################################################################################
##### Supplementary functions #####
##### January 2016 - ... , EMBL-EBI, N.Volkova ([email protected]) #####
################################################################################
round_dataframe <- function(df, n = 2) {
inds <- which(sapply(df,is.numeric))
for (j in inds) df[,j] <- round(df[,j],n)
return(df)
}
lenght <- function(x) {
message("Learn to spell it properly!")
return(length(x))
}
top <- function(x,n) {
return(sort(x,decreasing=T)[1:n])
}
which.top <- function(x,n) {
if (is.null(names(x))) return(order(x,decreasing=T)[1:n])
return(names(x)[order(x,decreasing=T)][1:n])
}
bottom <- function(x,n) {
return(sort(x,decreasing=F)[1:n])
}
which.bottom <- function(x,n) {
if (is.null(names(x))) return(order(x,decreasing=F)[1:n])
return(names(x)[order(x,decreasing=F)][1:n])
}
cosine <- function(x,y) {
return(sum(x * y) / sqrt(sum(x**2)) / sqrt(sum(y**2)))
}
divergence <- function (a,b) {
return (sum(a * log ( (a+.Machine$double.eps)/(b + .Machine$double.eps)) - a + b))
}
KL <- function(p,q) {
return(sum(p * log2((p+0.001)/(q+0.001))))
}
JSdistance <- function(p,q) {
M = 0.5*(p+q)
return (sqrt(0.5*KL(p,M) + 0.5*KL(q,M)))
}
restore <- function(x) {
t1 <- unlist(strsplit(x, split = '[:]'))
t2 <- c(t1[1],unlist(strsplit(t1[2], split = '[_]')))
t3 <- c(t2[1:2],unlist(strsplit(t2[3], split = '[/]')))
return(t3)
}
read_ce_vcf <- function(file, genome = "WBcel235") {
out <- tryCatch(
{
readVcf(file, genome=genome)
},
error=function(cond) {
message(paste("\nBad file in: ", file))
message("Here's the original error message:")
message(cond)
# Choose a return value in case of error
return(NA)
},
warning=function(cond) {
message(paste("\nFile caused a warning: ", file))
message("Here's the original warning message:")
message(cond)
# Choose a return value in case of warning
return(NULL)
}
)
return(out)
}
combination_check <- function(x,y) {
objective <- function(l) {
return(-as.numeric(cosine(y,x %*% t(t(l)))))
}
return(optim(par = rep(1,ncol(x)), objective, lower=rep(0,ncol(x))))
}
divergence <- function (a,b) {
return (a * log ( (a+.Machine$double.eps)/(b + .Machine$double.eps)) - a + b)
}
# supplementary functions
poisl <- function(X, theta, Y){
Yp <- X %*% theta
Y %*% log(Yp) - sum(Yp) - sum(log(factorial(Y)))
}
poisdl <- function(X, theta, Y){
lambda <- as.numeric(X %*% theta)
t(Y / lambda - 1) %*% X
}
poisI <- function(X, theta, Y){
lambda <- as.numeric(X %*% theta)
t(Y/lambda^2 * X) %*% X
}
poisL <- function(X, theta, Y){
Yp <- X %*% theta
prod(exp(-Yp)) * prod(Yp**Y) / prod(factorial(Y))
}
RevCom <- function(x) {
return(as.character(reverseComplement(DNAString(x))))
}
plot_all_changes <- function(plot_fc,S_est,beta_est,n = F) {
to.show <- data.frame(t(S_est))
for (j in 1:nrow(beta_est)) {
to.show <- cbind(to.show, S_est[nrow(S_est),] * exp(beta_est[j,]))
}
colnames(to.show) <- c(paste0('Sig',1:nrow(S_est)), paste0('Sig*beta',1:nrow(beta_est)))
plot_fc(to.show, norm = n)
}
plotRanges <- function(x, xlim = x, main = deparse(substitute(x)), col = "black", sep = 0.5, ...)
{
height <- 1
if (is(xlim, "Ranges"))
xlim <- c(min(start(xlim)), max(end(xlim)))
bins <- disjointBins(IRanges(start(x), end(x) + 1))
plot.new()
plot.window(xlim, c(0, max(bins)*(height + sep)))
ybottom <- bins * (sep + height) - height
rect(start(x)-0.5, ybottom, end(x)+0.5, ybottom + height, col = col, ...)
title(main)
axis(1)
}
getTrinucleotideSubs <- function(vcf, ref_genome="BSgenome.Celegans.UCSC.ce11") {
seqlevels(vcf) <- seqnames(get(ref_genome))
if (ref_genome==worm_ref_genome)
seqlevels(vcf) <- c("chrM","chrIV","chrIII","chrX","chrI","chrV","chrII")
vcf <- vcf[as.character(seqnames(vcf)) != "chrM"]
ranges = resize(vcf, 3, fix = "center")
tnc = as.character(getSeq(get(ref_genome), seqnames(vcf),
start(vcf) - 1, end(vcf) + 1))
s <- paste0(substr(tnc,1,1),"[",as.character(ref(vcf)), ">",
as.character(unlist(alt(vcf))),"]", substr(tnc,3,3))
n <- c("A","C","G","T")
f <- paste0(rep(n, each=4), "[", rep(n, each=96/2), ">", c(rep(c("C","G","T"), each=48/3),rep(c("A","G","T"), each=48/3),rep(c("A","C","T"), each=48/3), rep(c("A","C","G"), each=48/3)), "]", n)
s <- factor(s, levels=f)
return(s)
}
getTrinucleotideSubs_human_table <- function(subs, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19', chr = 0) {
g = get(ref_genome)
if (is.na(subs)) return(NA)
if (chr) subs <- subs[subs$Chrom != "chrM",] else subs <- subs[subs$Chrom != "MT",]
if (nrow(subs)==0) return(NA)
if (chr)
tnc = as.character(getSeq(g, subs$Chrom, subs$Pos - 1, subs$Pos + 1))
else
tnc = as.character(getSeq(g, paste('chr',subs$Chrom,sep=''),
subs$Pos - 1, subs$Pos + 1))
s <- paste0(substr(tnc,1,1),"[",as.character(subs$Ref), ">",
as.character(subs$Alt),"]", substr(tnc,3,3))
n <- c("A","C","G","T")
f <- paste0(rep(n, each=4), "[",
rep(n, each=96/2), ">",
c(rep(c("C","G","T"), each=16),
rep(c("A","G","T"), each=16),
rep(c("A","C","T"), each=16),
rep(c("A","C","G"), each=16)),
"]", n)
s <- factor(s, levels=f)
return(s)
}
getPentanucleotideSubs_human_table <- function(subs, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19') {
g = get(ref_genome)
if (is.na(subs)) return(NA)
subs <- subs[subs$Chrom != "MT",]
if (nrow(subs)==0) return(NA)
tnc = as.character(getSeq(g, paste('chr',subs$Chrom,sep=''),
subs$Pos - 2, subs$Pos + 2))
s <- paste0(substr(tnc,1,2),"[",as.character(subs$Ref), ">",
as.character(subs$Alt),"]", substr(tnc,4,5))
n <- c("A","C","G","T")
f <- paste0(rep(n, each=64),
rep(n, each=16),
"[",
rep(n, each=1536/2),
">",
c(rep(c("C","G","T"), each=256),
rep(c("A","G","T"), each=256),
rep(c("A","C","T"), each=256),
rep(c("A","C","G"), each=256)),
"]", rep(n, each = 4), n)
s <- factor(s, levels=f)
return(s)
}
tncToPyrimidine <- function(nucl) {
ind <- sort(c(grep('[G',nucl,fixed = T),grep('[A',nucl,fixed = T)))
newnucl <- as.character(reverseComplement(DNAStringSet(paste(substr(nucl[ind],1,1),
substr(nucl[ind],5,5),
substr(nucl[ind],3,3),
substr(nucl[ind],7,7),sep=''))))
nucl[ind] <- paste(substr(newnucl,1,1),'[',
substr(newnucl,2,2),'>',
substr(newnucl,3,3),']',
substr(newnucl,4,4),sep='')
return(nucl)
}
RevComMutType <- function(nucl) {
tmp <- unlist(strsplit(nucl, split = ''))
return(paste0(RevCom(tmp[7]),'[',RevCom(tmp[3]),'>',RevCom(tmp[5]),']',RevCom(tmp[1])))
}
pncToPyrimidine <- function(nucl) {
ind <- sort(c(grep('[G',nucl,fixed = T),grep('[A',nucl,fixed = T)))
newnucl <- as.character(reverseComplement(DNAStringSet(paste(substr(nucl[ind],1,2),
substr(nucl[ind],6,6),
substr(nucl[ind],4,4),
substr(nucl[ind],8,9),sep=''))))
nucl[ind] <- paste(substr(newnucl,1,2),'[',
substr(newnucl,3,3),'>',
substr(newnucl,4,4),']',
substr(newnucl,5,6),sep='')
return(nucl)
}
get_DNV_type <- function(vcf, ref_genome="BSgenome.Celegans.UCSC.ce11", dnv.types) {
s <- paste0(paste(as.character(ref(vcf)),collapse=''), ">", paste(as.character(unlist(alt(vcf))), collapse=''))
if (!(s %in% dnv.types)) {
s <- paste0(as.character(reverseComplement(DNAString(paste(as.character(ref(vcf)),collapse='')))), ">",
as.character(reverseComplement(DNAString(paste(as.character(unlist(alt(vcf))), collapse='')))))
}
return(s)
}
isMNV <- function(vcf) {
d <- diff(start(vcf)) == 1 & abs(diff(geno(vcf)$PM[,"TUMOUR"] )) <= 0.05
w <- c(FALSE, d) | c(d, FALSE)
return(w)
}
is.in.repeat <- function(vcf, ref_genome="BSgenome.Celegans.UCSC.ce11") {
seqlevels(vcf) <- c("chrM","chrIV","chrIII","chrX","chrI","chrV","chrII")
vcf <- vcf[as.character(seqnames(vcf)) != "chrM"]
#ranges = resize(vcf, 3, fix = "center")
in.repeat <- sapply(1:length(vcf), function(j) {
tmp <- vcf[j]
if (info(tmp)$PC=="DI") return(FALSE)
tnc = as.character(getSeq(get(ref_genome), seqnames(tmp),
start(tmp) - info(vcf)$LEN[j]*5,
end(tmp) + info(vcf)$LEN[j]*5))
if (info(tmp)$PC=="I")
return(grepl(paste0('(',substr(as.character(unlist(alt(tmp))), 2, nchar(as.character(unlist(alt(tmp))))),'){3,}'), tnc))
if (info(tmp)$PC=="D")
return(grepl(paste0('(',substr(as.character(ref(tmp)), 2, nchar(as.character(ref(tmp)))),'){3,}'), tnc))
return(FALSE)
})
return(in.repeat)
}
min_ranges <- function(gr) {
if (length(gr) == 1) return(gr)
to.merge <- 1
while (sum(to.merge)!=0) {
gr_start <- start(gr)
gr_end <- end(gr)
m = 1
to.merge <- vector('numeric',length(gr))
for (j in 2:length(gr)) {
if (gr_start[j] < gr_end[j-1]) {
if (gr_end[j] <= gr_end[j-1]) to.merge[j] <- -1
else {
to.merge[j] <- m
to.merge[j-1] <- m
m <- m+1
}
}
}
if (sum(to.merge==-1)>0) {
gr <- gr[-which(to.merge == -1)]
to.merge <- to.merge[-which(to.merge == -1)]
}
if (sum(to.merge>0)>0) {
for (j in 1:max(to.merge)) {
start(gr[to.merge == j]) <- min(gr_start[to.merge == j])
end(gr[to.merge == j]) <- min(gr_end[to.merge == j])
}
}
gr <- unique(gr)
}
return(gr)
}
`%over.50%` <- function(query, subject) overlapsAny(query, subject, minoverlap = 0.5 * min(width(query),width(subject)))
`%over.90%` <- function(query, subject) overlapsAny(query, subject, minoverlap = 0.9 * min(width(query),width(subject)))
duplicated.breakpoints <- function(SV) {
dupl <- rep(FALSE, nrow(SV))
for (j in 2:nrow(SV)) {
for (k in 1:(j-1)) {
if (SV$CHR1[j] == SV$CHR1[k] && SV$CHR2[j] == SV$CHR2[k] && SV$clust.type[j] == SV$clust.type[k]) {
if (SV$CHR1[j] != SV$CHR2[j]) {
iranges1 <- IRanges(start=c(as.numeric(SV$POS1)[j] - 50,as.numeric(SV$POS2)[j] - 50),
end=c(as.numeric(SV$POS1)[j] + 50,as.numeric(SV$POS2)[j] + 50))
iranges2 <- IRanges(start=c(as.numeric(SV$POS1)[k] - 50,as.numeric(SV$POS2)[k] - 50),
end=c(as.numeric(SV$POS1)[k] + 50,as.numeric(SV$POS2)[k] + 50))
if (iranges1[1] %over.90% iranges2[1] && iranges1[2] %over.90% iranges2[2]) {
dupl[j] <- TRUE
break
}
} else {
iranges <- IRanges(start=as.numeric(SV$POS1)[c(j,k)],end=as.numeric(SV$POS2)[c(j,k)])
if (iranges[1] %over.90% iranges[2]) {
dupl[j] <- TRUE
break
}
}
}
}
}
return(dupl)
}
filter.breakpoints <- function(SV, reference) {
reference$CHR1 <- as.character(reference$CHR1)
reference$CHR2 <- as.character(reference$CHR2)
reference$TYPE <- as.character(reference$TYPE)
if (is.na(SV) || nrow(SV)==0) return(SV)
bad <- NULL
SV$CHR1 <- as.character(SV$CHR1)
SV$CHR1 <- as.character(SV$CHR1)
SV$TYPE <- as.character(SV$TYPE)
`%over.50%` <- function(query, subject) overlapsAny(query, subject, minoverlap = 0.5 * min(width(query),width(subject)))
for (j in 1:nrow(SV)) {
tmp <- reference[reference$CHR1 == SV$CHR1[j] &
reference$CHR2 == SV$CHR2[j] &
reference$TYPE == SV$TYPE[j],,drop = F]
if (nrow(tmp) > 0) {
big.ranges.1 <- IRanges(start=as.numeric(tmp$POS1)-200,end=as.numeric(tmp$POS1)+200)
big.ranges.2 <- IRanges(start=as.numeric(tmp$POS2)-200,end=as.numeric(tmp$POS2)+200)
inds <- intersect(which(big.ranges.1 %over.50% IRanges(start=as.numeric(SV$POS1[j])-200,end=as.numeric(SV$POS1[j])+200)),
which(big.ranges.2 %over.50% IRanges(start=as.numeric(SV$POS2[j])-200,end=as.numeric(SV$POS2[j])+200)))
if (length(inds) > 0)
bad <- c(bad,j)
}
}
if (length(bad)>0)
return(SV[-bad,,drop=F])
return(SV)
}
GG_save_pdf = function(list, filename, ...) {
#start pdf
pdf(filename, ...)
#loop
count <- 1
for (p in list) {
print(p)
print(count)
count = count +1
}
#end pdf
dev.off()
invisible(NULL)
}
################################################################################
##### Supplementary functions #####
##### January 2016 - ... , EMBL-EBI, N.Volkova ([email protected]) #####
################################################################################
round_dataframe <- function(df, n = 2) {
inds <- which(sapply(df,is.numeric))
for (j in inds) df[,j] <- round(df[,j],n)
return(df)
}
lenght <- function(x) {
message("Learn to spell it properly!")
return(length(x))
}
top <- function(x,n) {
return(sort(x,decreasing=T)[1:n])
}
which.top <- function(x,n) {
if (is.null(names(x))) return(order(x,decreasing=T)[1:n])
return(names(x)[order(x,decreasing=T)][1:n])
}
bottom <- function(x,n) {
return(sort(x,decreasing=F)[1:n])
}
which.bottom <- function(x,n) {
if (is.null(names(x))) return(order(x,decreasing=F)[1:n])
return(names(x)[order(x,decreasing=F)][1:n])
}
cosine <- function(x,y) {
return(sum(x * y) / sqrt(sum(x**2)) / sqrt(sum(y**2)))
}
divergence <- function (a,b) {
return (sum(a * log ( (a+.Machine$double.eps)/(b + .Machine$double.eps)) - a + b))
}
KL <- function(p,q) {
return(sum(p * log2((p+0.001)/(q+0.001))))
}
JSdistance <- function(p,q) {
M = 0.5*(p+q)
return (sqrt(0.5*KL(p,M) + 0.5*KL(q,M)))
}
restore <- function(x) {
t1 <- unlist(strsplit(x, split = '[:]'))
t2 <- c(t1[1],unlist(strsplit(t1[2], split = '[_]')))
t3 <- c(t2[1:2],unlist(strsplit(t2[3], split = '[/]')))
return(t3)
}
read_ce_vcf <- function(file, genome = "WBcel235") {
out <- tryCatch(
{
readVcf(file, genome=genome)
},
error=function(cond) {
message(paste("\nBad file in: ", file))
message("Here's the original error message:")
message(cond)
# Choose a return value in case of error
return(NA)
},
warning=function(cond) {
message(paste("\nFile caused a warning: ", file))
message("Here's the original warning message:")
message(cond)
# Choose a return value in case of warning
return(NULL)
}
)
return(out)
}
combination_check <- function(x,y) {
objective <- function(l) {
return(-as.numeric(cosine(y,x %*% t(t(l)))))
}
return(optim(par = rep(1,ncol(x)), objective, lower=rep(0,ncol(x))))
}
divergence <- function (a,b) {
return (a * log ( (a+.Machine$double.eps)/(b + .Machine$double.eps)) - a + b)
}
# supplementary functions
poisl <- function(X, theta, Y){
Yp <- X %*% theta
Y %*% log(Yp) - sum(Yp) - sum(log(factorial(Y)))
}
poisdl <- function(X, theta, Y){
lambda <- as.numeric(X %*% theta)
t(Y / lambda - 1) %*% X
}
poisI <- function(X, theta, Y){
lambda <- as.numeric(X %*% theta)
t(Y/lambda^2 * X) %*% X
}
poisL <- function(X, theta, Y){
Yp <- X %*% theta
prod(exp(-Yp)) * prod(Yp**Y) / prod(factorial(Y))
}
RevCom <- function(x) {
return(as.character(reverseComplement(DNAString(x))))
}
plot_all_changes <- function(plot_fc,S_est,beta_est,n = F) {
to.show <- data.frame(t(S_est))
for (j in 1:nrow(beta_est)) {
to.show <- cbind(to.show, S_est[nrow(S_est),] * exp(beta_est[j,]))
}
colnames(to.show) <- c(paste0('Sig',1:nrow(S_est)), paste0('Sig*beta',1:nrow(beta_est)))
plot_fc(to.show, norm = n)
}
plotRanges <- function(x, xlim = x, main = deparse(substitute(x)), col = "black", sep = 0.5, ...)
{
height <- 1
if (is(xlim, "Ranges"))
xlim <- c(min(start(xlim)), max(end(xlim)))
bins <- disjointBins(IRanges(start(x), end(x) + 1))
plot.new()
plot.window(xlim, c(0, max(bins)*(height + sep)))
ybottom <- bins * (sep + height) - height
rect(start(x)-0.5, ybottom, end(x)+0.5, ybottom + height, col = col, ...)
title(main)
axis(1)
}
getTrinucleotideSubs <- function(vcf, ref_genome="BSgenome.Celegans.UCSC.ce11") {
seqlevels(vcf) <- seqnames(get(ref_genome))
if (ref_genome==worm_ref_genome)
seqlevels(vcf) <- c("chrM","chrIV","chrIII","chrX","chrI","chrV","chrII")
vcf <- vcf[as.character(seqnames(vcf)) != "chrM"]
ranges = resize(vcf, 3, fix = "center")
tnc = as.character(getSeq(get(ref_genome), seqnames(vcf),
start(vcf) - 1, end(vcf) + 1))
s <- paste0(substr(tnc,1,1),"[",as.character(ref(vcf)), ">",
as.character(unlist(alt(vcf))),"]", substr(tnc,3,3))
n <- c("A","C","G","T")
f <- paste0(rep(n, each=4), "[", rep(n, each=96/2), ">", c(rep(c("C","G","T"), each=48/3),rep(c("A","G","T"), each=48/3),rep(c("A","C","T"), each=48/3), rep(c("A","C","G"), each=48/3)), "]", n)
s <- factor(s, levels=f)
return(s)
}
getTrinucleotideSubs_human_table <- function(subs, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19', chr = 0) {
g = get(ref_genome)
if (is.na(subs)) return(NA)
if (chr) subs <- subs[subs$Chrom != "chrM",] else subs <- subs[subs$Chrom != "MT",]
if (nrow(subs)==0) return(NA)
if (chr)
tnc = as.character(getSeq(g, subs$Chrom, subs$Pos - 1, subs$Pos + 1))
else
tnc = as.character(getSeq(g, paste('chr',subs$Chrom,sep=''),
subs$Pos - 1, subs$Pos + 1))
s <- paste0(substr(tnc,1,1),"[",as.character(subs$Ref), ">",
as.character(subs$Alt),"]", substr(tnc,3,3))
n <- c("A","C","G","T")
f <- paste0(rep(n, each=4), "[",
rep(n, each=96/2), ">",
c(rep(c("C","G","T"), each=16),
rep(c("A","G","T"), each=16),
rep(c("A","C","T"), each=16),
rep(c("A","C","G"), each=16)),
"]", n)
s <- factor(s, levels=f)
return(s)
}
getPentanucleotideSubs_human_table <- function(subs, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19') {
g = get(ref_genome)
if (is.na(subs)) return(NA)
subs <- subs[subs$Chrom != "MT",]
if (nrow(subs)==0) return(NA)
tnc = as.character(getSeq(g, paste('chr',subs$Chrom,sep=''),
subs$Pos - 2, subs$Pos + 2))
s <- paste0(substr(tnc,1,2),"[",as.character(subs$Ref), ">",
as.character(subs$Alt),"]", substr(tnc,4,5))
n <- c("A","C","G","T")
f <- paste0(rep(n, each=64),
rep(n, each=16),
"[",
rep(n, each=1536/2),
">",
c(rep(c("C","G","T"), each=256),
rep(c("A","G","T"), each=256),
rep(c("A","C","T"), each=256),
rep(c("A","C","G"), each=256)),
"]", rep(n, each = 4), n)
s <- factor(s, levels=f)
return(s)
}
tncToPyrimidine <- function(nucl) {
ind <- sort(c(grep('[G',nucl,fixed = T),grep('[A',nucl,fixed = T)))
newnucl <- as.character(reverseComplement(DNAStringSet(paste(substr(nucl[ind],1,1),
substr(nucl[ind],5,5),
substr(nucl[ind],3,3),
substr(nucl[ind],7,7),sep=''))))
nucl[ind] <- paste(substr(newnucl,1,1),'[',
substr(newnucl,2,2),'>',
substr(newnucl,3,3),']',
substr(newnucl,4,4),sep='')
return(nucl)
}
RevComMutType <- function(nucl) {
tmp <- unlist(strsplit(nucl, split = ''))
return(paste0(RevCom(tmp[7]),'[',RevCom(tmp[3]),'>',RevCom(tmp[5]),']',RevCom(tmp[1])))
}
pncToPyrimidine <- function(nucl) {
ind <- sort(c(grep('[G',nucl,fixed = T),grep('[A',nucl,fixed = T)))
newnucl <- as.character(reverseComplement(DNAStringSet(paste(substr(nucl[ind],1,2),
substr(nucl[ind],6,6),
substr(nucl[ind],4,4),
substr(nucl[ind],8,9),sep=''))))
nucl[ind] <- paste(substr(newnucl,1,2),'[',
substr(newnucl,3,3),'>',
substr(newnucl,4,4),']',
substr(newnucl,5,6),sep='')
return(nucl)
}
get_DNV_type <- function(vcf, ref_genome="BSgenome.Celegans.UCSC.ce11", dnv.types) {
s <- paste0(paste(as.character(ref(vcf)),collapse=''), ">", paste(as.character(unlist(alt(vcf))), collapse=''))
if (!(s %in% dnv.types)) {
s <- paste0(as.character(reverseComplement(DNAString(paste(as.character(ref(vcf)),collapse='')))), ">",
as.character(reverseComplement(DNAString(paste(as.character(unlist(alt(vcf))), collapse='')))))
}
return(s)
}
isMNV <- function(vcf) {
d <- diff(start(vcf)) == 1 & abs(diff(geno(vcf)$PM[,"TUMOUR"] )) <= 0.05
w <- c(FALSE, d) | c(d, FALSE)
return(w)
}
is.in.repeat <- function(vcf, ref_genome="BSgenome.Celegans.UCSC.ce11") {
seqlevels(vcf) <- c("chrM","chrIV","chrIII","chrX","chrI","chrV","chrII")
vcf <- vcf[as.character(seqnames(vcf)) != "chrM"]
#ranges = resize(vcf, 3, fix = "center")
in.repeat <- sapply(1:length(vcf), function(j) {
tmp <- vcf[j]
if (info(tmp)$PC=="DI") return(FALSE)
tnc = as.character(getSeq(get(ref_genome), seqnames(tmp),
start(tmp) - info(vcf)$LEN[j]*5,
end(tmp) + info(vcf)$LEN[j]*5))
if (info(tmp)$PC=="I")
return(grepl(paste0('(',substr(as.character(unlist(alt(tmp))), 2, nchar(as.character(unlist(alt(tmp))))),'){3,}'), tnc))
if (info(tmp)$PC=="D")
return(grepl(paste0('(',substr(as.character(ref(tmp)), 2, nchar(as.character(ref(tmp)))),'){3,}'), tnc))
return(FALSE)
})
return(in.repeat)
}
min_ranges <- function(gr) {
if (length(gr) == 1) return(gr)
to.merge <- 1
while (sum(to.merge)!=0) {
gr_start <- start(gr)
gr_end <- end(gr)
m = 1
to.merge <- vector('numeric',length(gr))
for (j in 2:length(gr)) {
if (gr_start[j] < gr_end[j-1]) {
if (gr_end[j] <= gr_end[j-1]) to.merge[j] <- -1
else {
to.merge[j] <- m
to.merge[j-1] <- m
m <- m+1
}
}
}
if (sum(to.merge==-1)>0) {
gr <- gr[-which(to.merge == -1)]
to.merge <- to.merge[-which(to.merge == -1)]
}
if (sum(to.merge>0)>0) {
for (j in 1:max(to.merge)) {
start(gr[to.merge == j]) <- min(gr_start[to.merge == j])
end(gr[to.merge == j]) <- min(gr_end[to.merge == j])
}
}
gr <- unique(gr)
}
return(gr)
}
`%over.50%` <- function(query, subject) overlapsAny(query, subject, minoverlap = 0.5 * min(width(query),width(subject)))
`%over.90%` <- function(query, subject) overlapsAny(query, subject, minoverlap = 0.9 * min(width(query),width(subject)))
duplicated.breakpoints <- function(SV) {
dupl <- rep(FALSE, nrow(SV))
for (j in 2:nrow(SV)) {
for (k in 1:(j-1)) {
if (SV$CHR1[j] == SV$CHR1[k] && SV$CHR2[j] == SV$CHR2[k] && SV$clust.type[j] == SV$clust.type[k]) {
if (SV$CHR1[j] != SV$CHR2[j]) {
iranges1 <- IRanges(start=c(as.numeric(SV$POS1)[j] - 50,as.numeric(SV$POS2)[j] - 50),
end=c(as.numeric(SV$POS1)[j] + 50,as.numeric(SV$POS2)[j] + 50))
iranges2 <- IRanges(start=c(as.numeric(SV$POS1)[k] - 50,as.numeric(SV$POS2)[k] - 50),
end=c(as.numeric(SV$POS1)[k] + 50,as.numeric(SV$POS2)[k] + 50))
if (iranges1[1] %over.90% iranges2[1] && iranges1[2] %over.90% iranges2[2]) {
dupl[j] <- TRUE
break
}
} else {
iranges <- IRanges(start=as.numeric(SV$POS1)[c(j,k)],end=as.numeric(SV$POS2)[c(j,k)])
if (iranges[1] %over.90% iranges[2]) {
dupl[j] <- TRUE
break
}
}
}
}
}
return(dupl)
}
filter.breakpoints <- function(SV, reference) {
reference$CHR1 <- as.character(reference$CHR1)
reference$CHR2 <- as.character(reference$CHR2)
reference$TYPE <- as.character(reference$TYPE)
if (is.na(SV) || nrow(SV)==0) return(SV)
bad <- NULL
SV$CHR1 <- as.character(SV$CHR1)
SV$CHR1 <- as.character(SV$CHR1)
SV$TYPE <- as.character(SV$TYPE)
`%over.50%` <- function(query, subject) overlapsAny(query, subject, minoverlap = 0.5 * min(width(query),width(subject)))
for (j in 1:nrow(SV)) {
tmp <- reference[reference$CHR1 == SV$CHR1[j] &
reference$CHR2 == SV$CHR2[j] &
reference$TYPE == SV$TYPE[j],,drop = F]
if (nrow(tmp) > 0) {
big.ranges.1 <- IRanges(start=as.numeric(tmp$POS1)-200,end=as.numeric(tmp$POS1)+200)
big.ranges.2 <- IRanges(start=as.numeric(tmp$POS2)-200,end=as.numeric(tmp$POS2)+200)
inds <- intersect(which(big.ranges.1 %over.50% IRanges(start=as.numeric(SV$POS1[j])-200,end=as.numeric(SV$POS1[j])+200)),
which(big.ranges.2 %over.50% IRanges(start=as.numeric(SV$POS2[j])-200,end=as.numeric(SV$POS2[j])+200)))
if (length(inds) > 0)
bad <- c(bad,j)
}
}
if (length(bad)>0)
return(SV[-bad,,drop=F])
return(SV)
}
GG_save_pdf = function(list, filename, ...) {
#start pdf
pdf(filename, ...)
#loop
count <- 1
for (p in list) {
print(p)
print(count)
count = count +1
}
#end pdf
dev.off()
invisible(NULL)
}