aaa=c("HERC1")
bbb=c("MYO9A", "PKHD1L1", "PQLC2", "SLC7A2")
ccc=c("HERC1")
ddd=c("MACC1","PKHD1L1")

file_list = list(aaa = aaa, bbb = bbb, ccc = ccc, ddd = ddd)

max_file_len <- sapply(file_list, function(x) length(x)) %>% max()

result <- sapply(file_list, function(a) {
    length(a) <- max_file_len
    a
  }) %>%
  as.data.frame(stringsAsFactors = F) %>%
  gather() %>%
  filter(!is.na(value)) %>%
  expand(file_name = key, gene1 = value, gene2 = value) %>%
  filter(gene1 != gene2) %>%
  rowwise() %>%
  mutate(
    test = ifelse(
              (gene1 %in% file_list[[file_name]]) & (gene2 %in% file_list[[file_name]]),
              1, 0
           )
  ) %>%
  spread(file_name, test) %>%
  print(n = nrow(.))


# A tibble: 30 x 6
   gene1   gene2     aaa   bbb   ccc   ddd
   <chr>   <chr>   <dbl> <dbl> <dbl> <dbl>
 1 HERC1   MACC1       0  0        0  0
 2 HERC1   MYO9A       0  0        0  0
 3 HERC1   PKHD1L1     0  0        0  0
 4 HERC1   PQLC2       0  0        0  0
 5 HERC1   SLC7A2      0  0        0  0
 6 MACC1   HERC1       0  0        0  0
 7 MACC1   MYO9A       0  0        0  0
 8 MACC1   PKHD1L1     0  0        0  1.00
 9 MACC1   PQLC2       0  0        0  0
10 MACC1   SLC7A2      0  0        0  0
11 MYO9A   HERC1       0  0        0  0
12 MYO9A   MACC1       0  0        0  0
13 MYO9A   PKHD1L1     0  1.00     0  0
14 MYO9A   PQLC2       0  1.00     0  0
15 MYO9A   SLC7A2      0  1.00     0  0
16 PKHD1L1 HERC1       0  0        0  0
17 PKHD1L1 MACC1       0  0        0  1.00
18 PKHD1L1 MYO9A       0  1.00     0  0
19 PKHD1L1 PQLC2       0  1.00     0  0
20 PKHD1L1 SLC7A2      0  1.00     0  0
21 PQLC2   HERC1       0  0        0  0
22 PQLC2   MACC1       0  0        0  0
23 PQLC2   MYO9A       0  1.00     0  0
24 PQLC2   PKHD1L1     0  1.00     0  0
25 PQLC2   SLC7A2      0  1.00     0  0
26 SLC7A2  HERC1       0  0        0  0
27 SLC7A2  MACC1       0  0        0  0
28 SLC7A2  MYO9A       0  1.00     0  0
29 SLC7A2  PKHD1L1     0  1.00     0  0
30 SLC7A2  PQLC2       0  1.00     0  0