HI,
May be you should check this link
(http://r.789695.n4.nabble.com/R-overlapping-intervals-td810061.html).
dat1<-structure(list(chr = structure(c(1L, 1L, 1L, 2L, 2L, 2L), .Label = c("a",
"b"), class = "factor"), start = c(5, 30, 49, 70, 100, 129),
end = c(10, 52, 101, 103, 130, 140)), .Names = c("chr", "start",
"end"), row.names = c(NA, -6L), class = "data.frame")
Using Jim's code:
fun1<-function(x){
x1<-x2<-logical(max(x[,2],x[,3]))
x1[unlist(mapply(seq,x[,2],x[,3]))]<-TRUE
x2[unlist(mapply(seq,x[,2],x[,3]))]<-TRUE
r<-rle(x1 & x2)
offset<-cumsum(r$lengths)
cbind(offset[r$values]-r$lengths[r$values] +1,offset[r$values])}
list1<-lapply(split(dat1,dat1$chr),function(x) x)
res<-do.call(rbind,lapply(list1,function(x)
data.frame(chr=names(list1)[match.call()[[2]][[3]]],fun1(x))))
rownames(res)<-1:nrow(res)
colnames(res)<-colnames(dat1)
res
# chr start end
#1 a 5 10
#2 a 30 101
#3 b 70 140
A.K.
----- Original Message -----
From: Hermann Norpois <hnorp...@googlemail.com>
To: r-help@r-project.org
Cc:
Sent: Monday, November 5, 2012 12:14 PM
Subject: [R] fusion of overlapping intervals
Hello,
I have start and end coordinates from different experiments (DNase
hypersensitivity data) and now I would like to combine overlapping
intervals. For instance (see my test data below) (2) 30-52 and (3) 49-101
are combined to 30-101. But 49-101 and 70-103 would not be combined because
they are on different chromosomes (chr a and chr b).
Does anybody have an idea?
Thanks
Hermann
> df
chr start end
1 a 5 10
2 a 30 52
3 a 49 101
4 b 70 103
5 b 100 130
6 b 129 140
> dput (df)
structure(list(chr = structure(c(1L, 1L, 1L, 2L, 2L, 2L), .Label = c("a",
"b"), class = "factor"), start = c(5, 30, 49, 70, 100, 129),
end = c(10, 52, 101, 103, 130, 140)), .Names = c("chr", "start",
"end"), row.names = c(NA, -6L), class = "data.frame")
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