R-输出重叠间隔 [英] R - output overlapping intervals

问题描述

fileA包含间隔(开始，结束)和分配给该间隔的值(值).

fileA contains intervals (start, end), and a value assigned to that interval (value).

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的列表.我想从fileA检索重叠的间隔.开始和结束不一定匹配.这是fileB的示例:

fileB contains a list of the intervals I am interested in. I would like to retrieve the overlapping intervals from fileA. The starts and ends do not necessarily match. Here is an example of fileB:

start     end      label
77998     78005    romeo
78007     78012    juliet

目标是(1)从fileA检索与fileB重叠的间隔，以及(2)从fileB附加相应的标签.预期的结果是(#表示被丢弃的行，这是为了帮助可视化，并且不会出现在最终输出中):

The goal is to (1) retrieve the intervals from fileA that overlap with fileB and (2) to append the corresponding labels from fileB. The expected result is (# to designate the lines that were discarded, this is to help visualize and will not be in the final output):

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:

Here is my attempt at writing code:

#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)),]

在这一点上，我已经得到了意想不到的结果:

At this point I am already getting unexpected results:

> 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

我还没有写出输出标签的零件，因为我可能最好先解决这个问题，但是我无法弄清楚我出了什么问题...

I didn't write the part to output the labels yet because I might as well fix this first, but I can't figure out what I am getting wrong...

我也尝试了以下方法，但它只输出fileA的全部:

I also tried the following but it just outputs the entirety of fileA:

A_overlaps <- A[(min(A$start,A$end) < max(B$start,B$end)
               & max(A$start,A$end) > min(B$start,B$end)),]

推荐答案

这会产生所需的输出，但可能有点难以理解

This produces desired output, but may be a little difficult to read

# 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

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