I am interested in intersecting multiple lists of identifiers, making a table with the number of overlaps between pairs of lists ('rk' vs 't'). I have a vague idea that sapply is the way to go but I am still stuck after searching and reading tutorials.
rk1 <- list("YH_sensitive_933","CS_sensitive_1294","YH_sensitive_944","JB_persistent_1224","CS_sensitive_1299","YY_sensitive_922", "YH_sensitive_952","YA_sensitive_949")
rk2 <- list("YH_sensitive_944","JB_persistent_1224","CS_sensitive_1299","YY_sensitive_922", "YH_sensitive_952","YA_sensitive_949")
t1 <- list("YH_sensitive_933","CS_sensitive_1294","YH_sensitive_944")
t2 <- list("YH_sensitive_944","JB_persistent_1224")
t3 <- list("CS_sensitive_1299","YY_sensitive_922","YH_sensitive_944")
t4 <- list("YH_sensitive_952","YA_sensitive_949")
Edit: I thought maybe it'd best to group the two lists of lists and try sapply/mapply as suggested
F <- list(t1,t2,t3,t4)
G <- list(rk1,rk2)
> sapply(mapply(intersect,F,G), length)
[1] 3 2 3 2
but I'm a R beginner and would really appreciate some guidance on looping and using the apply functionals. But I only see the intersections for rk1 (but not rk2, which should be 1 2 3 2)
Using lapply/sapply
F <- list(t1, t2, t3, t4)
G <- list(rk1, rk2)
res <- do.call(`c`,setNames(lapply(G, function(.y)
setNames(sapply(F, `intersect`, .y), paste0("t",1:4))), paste0("rk",1:2)))
sapply(res, length)
#rk1.t1 rk1.t2 rk1.t3 rk1.t4 rk2.t1 rk2.t2 rk2.t3 rk2.t4
# 3 2 3 2 1 2 3 2
res$rk1.t1
#[[1]]
#[1] "YH_sensitive_933"
#[[2]]
#[1] "CS_sensitive_1294"
#[[3]]
#[1] "YH_sensitive_944"
intersect(rk1,t1)
#[[1]]
#[1] "YH_sensitive_933"
#[[2]]
#[1] "CS_sensitive_1294"
#[[3]]
#[1] "YH_sensitive_944"
res$rk2.t1
# [[1]]
#[1] "YH_sensitive_944"
intersect(rk2, t1)
#[[1]]
#[1] "YH_sensitive_944"
Or you could use mapply
(basic idea from @Richard Scriven's comment)
dat1 <- expand.grid(ls(pattern="^rk"), ls(pattern="^t"),stringsAsFactors=F)
res1 <- mapply(intersect, mget(dat1[,1]), mget(dat1[,2]))
res1[[1]]
#[[1]]
#[1] "YH_sensitive_933"
#[[2]]
#[1] "CS_sensitive_1294"
#[[3]]
#[1] "YH_sensitive_944"
To convert the res
to a matrix
mat1 <- do.call(cbind,lapply(lapply(res, unlist),
`length<-`, max(sapply(res, length))))
mat1
# rk1.t1 rk1.t2 rk1.t3
#[1,] "YH_sensitive_933" "YH_sensitive_944" "CS_sensitive_1299"
#[2,] "CS_sensitive_1294" "JB_persistent_1224" "YY_sensitive_922"
#[3,] "YH_sensitive_944" NA "YH_sensitive_944"
# rk1.t4 rk2.t1 rk2.t2
#[1,] "YH_sensitive_952" "YH_sensitive_944" "YH_sensitive_944"
#[2,] "YA_sensitive_949" NA "JB_persistent_1224"
#[3,] NA NA NA
# rk2.t3 rk2.t4
#[1,] "CS_sensitive_1299" "YH_sensitive_952"
#[2,] "YY_sensitive_922" "YA_sensitive_949"
#[3,] "YH_sensitive_944" NA
If you need to get the length
output in matrix,
resL <- sapply(res,length)
m1 <- matrix(resL, nrow=2, byrow=TRUE,
dimnames=list(paste0("rk", 1:2), paste0("t",1:4)))
m1
# t1 t2 t3 t4
#rk1 3 2 3 2
#rk2 1 2 3 2