Count the number of non-zero elements of each column

Question

Very new to R and I have a .rda file that contains a matrix of gene IDs and counts for each ID in 96 columns. It looks like this:

I want to get separate counts for the number of non-zero items in each column. I've been trying the sum() function in a loop, but perhaps I don't understand loop syntax in R. Any help appreciated. Thanks!

Forest

Answer 1

What about:

apply(your.matrix, 2, function(c)sum(c!=0)) 

Does this help?

edit:

Even better:

colSums(your.matrix != 0) 

edit 2:

Here we go, with an example for ya:

> example = matrix(sample(c(0,0,0,100),size=70,replace=T),ncol=7) > example       [,1] [,2] [,3] [,4] [,5] [,6] [,7]  [1,]    0  100    0    0  100    0  100  [2,]  100    0    0    0    0    0  100  [3,]    0    0    0    0    0    0  100  [4,]    0  100    0    0    0    0    0  [5,]    0    0  100  100    0    0    0  [6,]    0    0    0  100    0    0    0  [7,]    0  100  100    0    0    0    0  [8,]  100    0    0    0    0    0    0  [9,]  100  100    0    0  100    0    0 [10,]    0    0    0    0    0  100    0 > colSums(example != 0) [1] 3 4 2 2 2 1 3 

(new example, the previous example with '1' values was not suited to show that we are summing the number of cells, not their contents)

Answer 2

with x being a column or vector;

length(which(x != 0))