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Count non-zero elements along the column and append to table in R

I have a table like this,

gene1 a 2 0 1 0
gene2 b 5 0 2 2
gene3 a 7 4 0 0

I want to count the number of non-zero elements in rows and columns and append it to the same table. This is how I did it for rows: myfile$rowsum <- rowSums(myfile[4:6] != 0). For columns I am trying to make this one work, but it starts from the 1st column and not the 4th: rbind(myfile, colSums(myfile != 0)) Not sure how to append it and how to move starting from column 4. So i want something like this 

gene1 a 2 0 1 0 1
gene2 b 5 0 2 2 2
gene3 a 7 4 0 0 1
          1 2 1
r
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updated by avaneesh.t • avaneesh.t • written by User000 User000

2 answers

This is how I did it for rows: myfile$rowsum <- rowSums(myfile[4:6] !=0)

Shouldn't it be rowSums(myfile[,4:6]) ?

For columns I am trying to make this one work, but it starts from the 1st column and not the 4th: rbind(myfile, colSums(myfile != 0))

Try rbind(myfile, c("colsum", "NA", "NA", colSums(myfile[,4:6] != 0)))

• 0 views • link
written by Carlo Yague Carlo Yague

This is working, thanks!

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written by User000 User000

Here's what I came up with - there are probably much better ways of doing this. 

 > zeros <- which(table ==0, arr.ind = T)

      row col
 [1,]   1   4
 [2,]   2   4
 [3,]   3   5
 [4,]   1   6
 [5,]   3   6
  
 > colcount = array(0,dim = ncol(table)-1)
 > rowcount = array(0,dim = nrow(table))
 > for(i in b[,2]){colcount[i-1]=colcount[i-1]+1}
 > for(i in b[,1]){rowcount[i]=rowcount[i]+1}

 > b <- cbind(table,rowcount)
 > b <- rbind(b,c("",colcount,""))

giving you 

 b
                                 rowcount
 [1,] "gene1" "a" "2" "0" "1" "0" "2"     
 [2,] "gene2" "b" "5" "0" "2" "2" "1"     
 [3,] "gene3" "a" "7" "4" "0" "0" "2"     
 [4,] ""      "0" "0" "4" "2" "4" ""
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written by avaneesh.t • avaneesh.t

Shouldn't rows 2 and 4 rowcount be 3?

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written by theobroma22 theobroma22

actually, it should be 1,2,1. I just noticed the output is completely wrong...

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written by User000 User000

Yeah - I'm not sure how that happened. Sorry!

• 0 views • link
written by avaneesh.t • avaneesh.t

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