问题
have a list of files that contain specific genes, and I want to create a binary relation matrix in R that shows the presence of each gene in each file.
For example, here are my files aaa
, bbb
, ccc
, and ddd
and the genes associated to them.
aaa=c("HERC1")
bbb=c("MYO9A", "PKHD1L1", "PQLC2", "SLC7A2")
ccc=c("HERC1")
ddd=c("MACC1","PKHD1L1")
I need to generate another table that where, for each pair of genes, I assign the value 1 if both of them present in the specific file, and 0 other wise. Following the example that I gave earlier, this new table should look like the following one:
Does anybody know a quick way to obtain this new bigenic table in R? Thanks!
回答1:
Assuming you can read the the files into a named list, here's one way using tidyverse
-
file_list <- list(aaa = aaa, bbb = bbb, ccc = ccc, ddd = ddd)
result <- stack(file_list) %>%
inner_join(stack(file_list), by = c("ind" = "ind")) %>%
select(gene1 = values.x, gene2 = values.y, file_name = ind) %>%
mutate(n = 1) %>%
complete(gene1, gene2, file_name, fill = list(n = 0)) %>%
filter(gene1 != gene2,
!duplicated(
apply(., 1, function(x) paste0(sort(x), collapse = ""))
)
) %>%
spread(file_name, n)
# A tibble: 15 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 MYO9A 0 0 0 0
7 MACC1 PKHD1L1 0 0 0 1
8 MACC1 PQLC2 0 0 0 0
9 MACC1 SLC7A2 0 0 0 0
10 MYO9A PKHD1L1 0 1 0 0
11 MYO9A PQLC2 0 1 0 0
12 MYO9A SLC7A2 0 1 0 0
13 PKHD1L1 PQLC2 0 1 0 0
14 PKHD1L1 SLC7A2 0 1 0 0
15 PQLC2 SLC7A2 0 1 0 0
来源:https://stackoverflow.com/questions/56193505/how-to-create-a-binary-relation-matrix-of-pair-occurrences-from-a-list-of-string