fileA
包含间隔(开始,结束)和分配给该间隔(值)的值。
start end value
0 123 1 #value 1 at positions 0 to 122 included.
123 78000 0 #value 0 at positions 123 to 77999 included.
78000 78004 56 #value 56 at positions 78000, 78001, 78002 and 78003.
78004 78005 12 #value 12 at position 78004.
78005 78006 1 #value 1 at position 78005.
78006 78008 21 #value 21 at positions 78006 and 78007.
78008 78056 8 #value 8 at positions 78008 to 78055 included.
78056 81000 0 #value 0 at positions 78056 to 80999 included.
fileB
包含我感兴趣的区间列表。我想从fileA
检索重叠区间。开始和结束不一定匹配。以下是fileB
的示例:
start end label
77998 78005 romeo
78007 78012 juliet
目标是(1)从fileA
检索与fileB
和(2)重叠的区间,以附加fileB
的相应标签。预期的结果是(#指定被丢弃的行,这是为了帮助可视化并且不会在最终输出中):
start end value label
#
123 78000 0 romeo
78000 78004 56 romeo
78004 78005 12 romeo
#
78006 78008 21 juliet
78008 78056 8 juliet
#
这是我编写代码的尝试:
#read from tab-delimited text files which do not contain column names
A<-read.table("fileA.txt",sep="\t",colClasses=c("numeric","numeric","numeric"))
B<-read.table("fileB.txt",sep="\t",colClasses=c("numeric","numeric","character"))
#add column names
colnames(A)<-c("start","end","value")
colnames(B)<-c("start","end","label")
#output intervals in `fileA` that overlap with an interval in `fileB`
A_overlaps<-A[((A$start <= B$start & A$end >= B$start)
|(A$start >= B$start & A$start <= B$end)
|(A$end >= B$start & A$end <= B$end)),]
此时我已经得到了意想不到的结果:
> A_overlaps
start end value
#missing
3 78000 78004 56
5 78005 78006 1 #this line should not be here
6 78006 78008 21
#missing
我没有写部件来输出标签,因为我不妨先解决这个问题,但我无法弄清楚我的错误......
[编辑]
我也尝试了以下内容,但它只输出fileA
的全部内容:
A_overlaps <- A[(min(A$start,A$end) < max(B$start,B$end)
& max(A$start,A$end) > min(B$start,B$end)),]
答案 0 :(得分:1)
这会产生所需的输出,但可能有点难以阅读
# function to find, if value lies in interval
is.between <- function(x, a, b) {
(x - a) * (b - x) > 0
}
# apply to all rows in A
> matching <- apply(A, MARGIN=1, FUN=function(x){
# which row fulfill following condition:
+ which(apply(B, MARGIN=1, FUN=function(y){
# first value lies in interval from B or second value lies in interval from B
+ is.between(as.numeric(x[1]), as.numeric(y[1]), as.numeric(y[2])) | is.between(as.numeric(x[2]), as.numeric(y[1]), as.numeric(y[2]))
+ }))
+ })
>
# print the results
> matching
[[1]]
integer(0)
[[2]]
[1] 1
[[3]]
[1] 1
[[4]]
[1] 1
[[5]]
integer(0)
[[6]]
[1] 2
[[7]]
[1] 2
[[8]]
integer(0)
>
# filter those, which has 0 length = no matching
> A_overlaps <- A[unlist(lapply(matching, FUN=function(x)length(x)>0)),]
# add label
> A_overlaps$label <- B$label[unlist(matching)]
>
> A_overlaps
start end value label
2 123 78000 0 romeo
3 78000 78004 56 romeo
4 78004 78005 12 romeo
6 78006 78008 21 juliet
7 78008 78056 8 juliet