Find matching elements based on multiple arguments in R

Question

I have a large data frame that looks like this. I want to find which genes match the others based on an overlap between the start and end positions.

library(tidyverse)

data <- data.frame(group=c(1,1,1,2,2,2),
                     genes=c("A","B","C","D","E","F"), 
                     start=c(1000,2000,3000,800,400,2000),
                     end=c(1500,2500,3500,1200,500,10000))

data
#>   group genes start   end
#> 1     1     A  1000  1500
#> 2     1     B  2000  2500
#> 3     1     C  3000  3500
#> 4     2     D   800  1200
#> 5     2     E   400   500
#> 6     2     F  2000 10000

^{Created on 2022-12-05 with reprex v2.0.2}

I want something like this.

data
#>   group genes start   end   match
#> 1     1     A  1000  1500    A-D
#> 2     1     B  2000  2500    B-F
#> 3     1     C  3000  3500    C-F
#> 4     2     D   800  1200    A-D
#> 5     2     E   400   500    NA
#> 6     2     F  2000 10000    F-C-B

I am a bit lost on how to start. Any help is appreciated

Should row 5 (genes="E") be matched to itself? Does "group" have any relevance here? — njp, Dec 04 '22 at 23:25
Possible duplicate https://stackoverflow.com/q/24480031/680068 — zx8754, Jan 03 '23 at 09:40

score 2 · Accepted Answer · answered Dec 04 '22 at 23:27

With devel version of dplyr, we can use

library(dplyr)
library(stringr)
by <- join_by(overlaps(x$start, x$end, y$start, y$end))
full_join(data, data, by) %>% 
  group_by(genes= genes.x) %>% 
  summarise(match = if(n() ==1) NA_character_ else 
      str_c(genes.y, collapse = '-')) %>%
 left_join(data, .)

-output

  group genes start   end match
1     1     A  1000  1500   A-D
2     1     B  2000  2500   B-F
3     1     C  3000  3500   C-F
4     2     D   800  1200   A-D
5     2     E   400   500  <NA>
6     2     F  2000 10000 B-C-F

Find matching elements based on multiple arguments in R

1 Answers1