子集一个表，通过两个列在R中的查找表中的任何参考范围内

发布于 2025-02-08 21:49:09 字数 646 浏览 3 评论 0原文

R TABLE1：实际上还有更多行

PatientID chr pos  type end  length 
AB1       1  2431  DEL 2100  -331
AC3       1  98041 INV 99100  1059
AG6       1  8743  BND 9000   257

表2：实际上，更多的行，第2和3列是外显子所需输出的范围

Exon 2001 2500 
Exon 8700 8750

：从表1中的那些行，其中变体的任何部分（来自pos-end）（来自pos-end）属于任何地方在Table2输出中的外显子的范围中

：

PatientID chr pos  type end   length 
AB1       1  2431  DEL 2100  -331
AG6       1  8743  BND 9000   257

我尝试了一个子集：

subset(table1$pos >= table2$V2 | table1$end <= table$end)

但这并不能给我所需的输出。任何帮助都将不胜感激。

一切顺利

原文

R Table1: In reality many more rows

PatientID chr pos  type end  length 
AB1       1  2431  DEL 2100  -331
AC3       1  98041 INV 99100  1059
AG6       1  8743  BND 9000   257

Table 2: In reality many more rows, columns 2 and 3 are the ranges for the exon

Exon 2001 2500 
Exon 8700 8750

Desired output: Those rows from table 1 where any part of the variants (from pos-end) fall within anywhere of the range of an Exon in table2

output:

PatientID chr pos  type end   length 
AB1       1  2431  DEL 2100  -331
AG6       1  8743  BND 9000   257

I have tried a subset:

subset(table1$pos >= table2$V2 | table1$end <= table$end)

but this does not give me my desired output. Any help would be much appreciated.

All the best

分享到QQ

分享到微博

如果你对这篇内容有疑问，欢迎到本站社区发帖提问参与讨论，获取更多帮助，或者扫码二维码加入 Web 技术交流群。

发布评论

需要登录才能够评论，你可以免费注册一个本站的账号。

愁杀 2025-02-15 21:49:10

如果我正确理解您，您想找到的变体（对于Table2至少一个范围， r ）至少满足以下条件之一：

table1 $ end end is在 r
表1 $ pos在 r
table1 中下面的 r 的相对侧是对

所有可能性的示意图描述，这些可能性是由括号界定的 r ，以及由连字符代表的变体以及符合条件的数量。

-[-  ]   1.
 [  -]-  2.
 [ - ]   1. and 2.
-[---]-  3.

请注意，下面的代码假定（与Table1）Table2 [，2]＆lt; = table2 [，3]。

# simplified table1
table1 <- data.frame(pos=c(2431, 98041, 8743), end=c(2100, 99100, 9000))
table2 <- data.frame(exon='Exon', from=c(2001, 8700), to=c(2500, 8750))

is.within <- apply(table1[, c('pos', 'end')], 1, function(x) {
  
  x <- sort(x)  # make sure x[1] <= x[2], i.e. pos <= end
  any((x[1] >= table2[, 2] & x[1] <= table2[, 3]) |      # 1.
        (x[2] >= table2[, 2] & x[2] <= table2[, 3]) |    # 2.
        (x[1] <= table2[, 2] & x[2] >= table2[, 3]))     # 3.
        
})
table1[is.within, ]

If I understand you correctly, you want to find variants which (for at least one range in table2, r) meet at least one of the following conditions:

table1$end is within r
table1$pos is within r
table1$pos and table2$end are on opposite sides of r

Below are schematic depictions of all possibilities with r delimited by brackets and a variant represented by hyphens together with the numbers of conditions met.

-[-  ]   1.
 [  -]-  2.
 [ - ]   1. and 2.
-[---]-  3.

Please note that the code below assumes that (unlike table1) table2[, 2] <= table2[, 3].

# simplified table1
table1 <- data.frame(pos=c(2431, 98041, 8743), end=c(2100, 99100, 9000))
table2 <- data.frame(exon='Exon', from=c(2001, 8700), to=c(2500, 8750))

is.within <- apply(table1[, c('pos', 'end')], 1, function(x) {
  
  x <- sort(x)  # make sure x[1] <= x[2], i.e. pos <= end
  any((x[1] >= table2[, 2] & x[1] <= table2[, 3]) |      # 1.
        (x[2] >= table2[, 2] & x[2] <= table2[, 3]) |    # 2.
        (x[1] <= table2[, 2] & x[2] >= table2[, 3]))     # 3.
        
})
table1[is.within, ]

回复收藏 0 原文

~没有更多了~