Looking for a quick way to combine rows in a matrix

You can automate this step

key[key == "AT"] <- "TA"

## create a function to reverse a string -- see strsplit help page for this
strReverse function
reverse <- function(x) sapply(lapply(strsplit(x, NULL), rev), paste,
collapse="")

key <- rownames(a)
# combine rownames with reverse (rownames)
n<-cbind(key, rev=reverse(key))
     key  rev 
[1,] "AA" "AA"
[2,] "AT" "TA"
[3,] "TA" "AT"
[4,] "TT" "TT"

# Now just sort the values in the rows   (apply returns column vectors so I
also use t() ) and then run do.call on first column
 n<-t(apply(n,1, sort))

do.call(rbind, by(a, n[,1], colSums)) 
   V1 V2 V3 V4
AA  1  5  9 13
AT  5 13 21 29
TT  4  8 12 16


I often need to combine reverse complement DNA strings, so you could do that
too 

# DNA complement
comp <-  function(x) chartr("ACGT", "TGCA", x)

n<-cbind(key, rev=reverse(comp(key)))  
 n<-t(apply(n,1, sort))
do.call(rbind, by(a, n[,1], colSums)) 
   V1 V2 V3 V4
AA  5 13 21 29   
AT  2  6 10 14
TA  3  7 11 15


Chris Stubben

Try this:

key <- rownames(a)
key[key == "AT"] <- "TA"
do.call(rbind, by(a, key, colSums))

   V2 V3 V4 V5
AA  1  5  9 13
TA  5 13 21 29
TT  4  8 12 16


On Mon, May 11, 2009 at 4:53 PM, Crosby, Jacy R
<Jacy.R.Crosby at uth.tmc.edu>wrote:

I'm working with genotype data in a frequency table:

a=matrix(1:16, nrow=4)
rownames(a)=c("AA","AT","TA","TT")
a

  [,1] [,2] [,3] [,4]
AA    1    5    9   13
AT    2    6   10   14
TA    3    7   11   15
TT    4    8   12   16

'AT' and 'TA' are essentially the same, and I'd like to combine (add) the
rows to reflect this. The final matrix should be:

  [,1] [,2] [,3] [,4]
AA    1    5    9   13
AT    5    13   21   29
TT    4    8   12   16

Is there a fast way to do this?

Thanks in advance!

Jacy Crosby
jacy.r.crosby at uth.tmc.edu

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