fileA
包含间隔(开始、结束)以及分配给该间隔的值(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
包含我感兴趣的间隔列表。我想从中检索重叠间隔fileA
。开始和结束不一定匹配。这是一个例子fileB
:
start end label
77998 78005 romeo
78007 78012 juliet
目标是 (1) 检索区间fileA
与重叠的fileB
(2) 附加相应的标签fileB
。预期结果是(# 指定被丢弃的行,这是为了帮助可视化,并且不会出现在最终输出中):
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
我还没有编写输出标签的部分,因为我不妨先解决这个问题,但我不知道我错了什么......
[编辑]
我也尝试了以下方法,但它只输出全部fileA
:
A_overlaps <- A[(min(A$start,A$end) < max(B$start,B$end)
& max(A$start,A$end) > min(B$start,B$end)),]