find most frequent subset in dataframe

Question

So I have the following dataframe:

and what I want is to find the combination of genes that are present together the most.

  sample genea geneb genec gened genee genef
1      1     1     1     1     0     0     0
2      2     1     1     1     0     0     0
3      3     1     0     0     1     1     1
4      4     0     0     0     0     0     0
5      5     1     0     1     1     1     1
6      6     0     0     0     0     0     0

so in this case, my desired output would be: gene a + c = 3 samples overlap.

test[sort.list(colSums(test[,-1]), decreasing=TRUE)[1:15] +1]) gives me a list with most 1 values per gene. But I am getting stuck with this.

How do I approach this.

Answer 1

One way would be to use crossprod():

library(tidyr)
library(dplyr)

dat %>%
  pivot_longer(-sample) %>%
  filter(value == 1) %>%
  select(-value) %>%
  table() %>%
  crossprod() %>%
  replace(lower.tri(., diag = TRUE), NA) %>%
  as.data.frame.table() %>%
  slice_max(Freq)

   name name.1 Freq
1 genea  genec    3