R - I want to go through rows of a big matrix and remove all zeros

Question

I have a lot of rows and columns in a very large matrix (184 x 4000, type double), and I want to remove all 0\'s. The values in the matrix are usually greater than 0 but the

Answer 1

You could try:

x[!rowSums(!x)==ncol(x),] #could be shortened to

x[!!rowSums(abs(x)),] #Inspired from @Richard Scriven

data

 x <- structure(list(V1 = c(2, 0, 2, 2, 2, 3, 2, 0, 0, 3), V2 = c(2, 
   0, 0, 2, 3, 1, 0, 0, 0, 0), V3 = c(3, 0, 1, 3, 3, 2, 0, 3, 0, 
  1), V4 = c(3, 0, 2, 3, 2, 2, 2, 1, 2, 1), V5 = c(0, 0, 0, 0, 
  1, 2, 2, 2, 1, 3)), .Names = c("V1", "V2", "V3", "V4", "V5"), row.names = c(NA, 
  -10L), class = "data.frame")

 

• !x. Creates a logical index of TRUE and FALSE, where TRUE will be elements that are 0's
• rowSums(!x). rowwise Sum of those TRUEs,
• ==ncol(x). Check whether the sum is equal to the number of columns. In the above example it is 5. That means all entries are 0
• ! Negate again because we want to filter out these rows
• Subset x using this logical index

Update

Suppose you have NA's in your dataset and you want to remove rows with all 0's or those with 0's and NA's, for e.g.

 x <-   structure(list(V1 = c(2, 0, 2, 2, 2, 3, 2, 0, 0, 3), V2 = c(2, 
 NA, 0, 2, 3, 1, 0, 0, 0, 0), V3 = c(3, 0, 1, 3, 3, 2, 0, 3, 0, 
 1), V4 = c(3, 0, 2, 3, 2, 2, NA, 1, 2, 1), V5 = c(0, 0, 0, 0, 
 1, 2, 2, 2, 1, 3)), .Names = c("V1", "V2", "V3", "V4", "V5"), row.names = c(NA, 
 -10L), class = "data.frame")

 x[!(rowSums(!is.na(x) & !x)+rowSums(is.na(x)))==ncol(x),]

• The idea is to first sum the NAs rowwise

• Rowwise sum of all the elements that are not NAs and are 0's rowSUms(!is.na(x) & !x)

• Take the sum of the above two. If that number matches with the number of columns, delete that row