R: Adding two matrices with different dimensions based on columns

Question

I have 22 matrices having equal number of rows (i.e. 691) and different number of columns (i.e. 22-25). I have to add the values corresponding to same row, same column in each of the matrices resulting in one single matrix of the dimension 691*25.

fullanno1 has 691 rows & 25 columns:
>colnames(fullanno1)
[1] "coding-notMod3"                "coding-synonymous"             "coding-synonymous-near-splice"
[4] "intergenic"                    "intron"                        "missense"                     
[7] "missense-near-splice"          "near-gene-3"                   "near-gene-5"                  
[10] "splice-3"                      "splice-5"                      "stop-gained"                  
[13] "stop-gained-near-splice"       "stop-lost"                     "utr-3"                        
[16] "utr-5"                         "CTCF"                          "E"                            
[19] "None"                          "PF"                            "R"                            
[22] "T"                             "TSS"                           "WE"                           
[25] "coding-notMod3-near-splice"   

fullanno2 has 691 rows and 22 columns:
>colnames(fullanno2)

[1] "coding-synonymous"             "coding-synonymous-near-splice" "intergenic"                   
[4] "intron"                        "missense"                      "missense-near-splice"         
[7] "near-gene-3"                   "near-gene-5"                   "splice-3"                     
[10] "splice-5"                      "stop-gained"                   "stop-lost"                    
[13] "utr-3"                         "utr-5"                         "CTCF"                         
[16] "E"                             "None"                          "PF"                           
[19] "R"                             "T"                             "TSS"                          
[22] "WE"

Each matrix is a double matrix with numerical values. How can I add these two matrices such that I get a third matrix with dimensions 691*25. Because fullanno2 is three columns short, for those columns the resulting matrix will have values only from the first matrix.

My approach: Take a setdiff of the colnames to get columns that are not present in the smaller matrix, cbind them to the smaller matrix with 0s as values. Then add the two matrices.

> column.names<-setdiff(colnames(fullanno1),colnames(fullanno2))
[1] "coding-notMod3"             "stop-gained-near-splice"    "coding-notMod3-near-splice"
> column<-0
>cbind(fullanno2,column)
>colnames(fullanno2)[23]<-column.name[1]
>cbind(fullanno2,column)
>colnames(fullanno2)[24]<-column.name[2]
>cbind(fullanno2,column)
>colnames(fullanno2)[25]<-column.name[3]

But this is getting tedious for all the matrices. Any suggestions?

Peyton Peyton · Accepted Answer · 2013-10-12T18:12:09

So you want to sum all of the matrices to end up with one matrix? A simple but perhaps slow (I suspect, but it's probably not a big deal with your matrices) way is to use the plyr and reshape2 libraries. You could start with a list of your matrices:

make.matrix <- function() {
  cols <- sample(month.name, runif(1, 2, 12))
  matrix(rnorm(length(cols)*10), 10, length(cols), dimnames=list(NULL, cols))
}

# Make 10 matrices filled with random numbers, having
# varying numbers of columns named after months
my.matrices <- replicate(10, make.matrix())

Then you can melt all the matrices into one big dataframe

matrix.df <- ldply(my.matrices, melt, varnames=c("row", "col"))
head(matrix.df)
#   row      col      value
# 1   1 February -0.4239145
# 2   2 February  1.1773608
# 3   3 February -2.9565403
# 4   4 February  0.3955096
# 5   5 February -0.3784917
# 6   6 February -0.6234579

and then cast it back into a matrix.

sum.matrix <- acast(matrix.df, row ~ col, sum)

R: Adding two matrices with different dimensions based on columns

2 Answers