NA won't omit in R when 0 is between 1's - r

Question

I am suppose to change a square matrix which represents a graph (the vertices-and-edges kind) and change it into a list that represents the same graph
square matrix: element (i,j) = 1 means there is an edge i -> j
list: element i is a vector (possibly empty, coded as NA) of all j s.t. there is an edge i -> j
My problem is that if there is a zero in the middle of the row it returns a NA and it is only suppose to do that when a vector is empty(no edges). It only does it when a zero is between two 1's. I don't know why and NA.omit doesn't work.
This is my first time programming in R.
squaretolist <- function(m){
ml <- list() #creates an empty list that we will return at the end
for(i in 1:ncol(m)){ #loop through columns
b1 <- c()
for(j in 1:nrow(m)){ #loop through rows
ifelse(m[i,j] %in% 1, b1[j] <- j, next)
}
ifelse(length(b1) == 0, ml[[i]]<- NA, ml[[i]] <- b1 )
}
return(ml)
}

Answer 1

In your function, if you have a zero in between two 1s, for example 1 in the 1st position and in the 3rd position, you're assigning b1[1] to 1, b1[3] to 3 but, as you have a 0 in the 2nd position, you're not assigning b1[2] to anything so it becomes NA.
To avoid that, you can replace ifelse(m[i,j] %in% 1, b1[j] <- j, next)
by ifelse(m[i,j] %in% 1, b1 <- c(b1,j), next).
You can also get what you want with the use of grep and apply functions :
ml <- apply(m, 1, function(i) {if(any(i==1)) grep(1, i) else NA})
This instruction tells R to apply, for each row of the matrix m, a function that returns, if there is at least one 1, the position of the 1(s), else NA.
Example:
set.seed(123)
m<-matrix(sample(c(0,1),25,replace=T),nrow=5)
m[4,]<-rep(0,5)
# > m
# [,1] [,2] [,3] [,4] [,5]
# [1,] 0 0 1 1 1
# [2,] 1 1 0 0 1
# [3,] 0 1 1 0 1
# [4,] 0 0 0 0 0
# [5,] 1 0 0 1 1
ml<-apply(m,1,function(i){if(any(i==1)) grep(1,i) else NA})
# > ml
# [[1]]
# [1] 3 4 5
# [[2]]
# [1] 1 2 5
# [[3]]
# [1] 2 3 5
# [[4]]
# [1] NA
# [[5]]
# [1] 1 4 5