R help - Mar 2012 - extract same columns and rows in two matrices

Hello,

I have two matrices. They both have different row names and column names,
but they have some common row names and column names. The row names and
column names that are the same are what I am interested in. I also want the
columns in the two matrices aligned the same. In the end, I need to do
rd[1,1] and ua[1,1], for example and be accessing the same column and row
for both matrices.  Thank you very much for all you help.

I can do it, but I am pretty sure there is a better/faster way:

################ make some sample data
ua = matrix(c(1,2,3,4,5,6),nrow=2,ncol=3)
colnames(ua) = c('a','b','c')
rownames(ua)= c('ra','rb')
rd1 = matrix(c(7,8,9,10,11,12,13,14,15,16,17,18),nrow=3,ncol=4)
colnames(rd1) = c('c','b','a','d')
rownames(rd1)= c('rc','rb','ra')
> rd1
c  b  a  d
rc 7 10 13 16
rb 8 11 14 17
ra 9 12 15 18
> ua
a b c
ra 1 3 5
rb 2 4 6

##################### get common columns and rows and order them the same,
this works but is slow'ish
rd1_cn = colnames(rd1)
ua_cn = colnames(ua)
common_t = merge(rd1_cn,ua_cn,by.x=1,by.y=1)
common_t = as.character(common_t[,1])
rd1 = rd1[,common_t]
ua = ua[,common_t]
rd1_d = rownames(rd1)
ua_d = rownames(ua)
common_d = merge(rd1_d,ua_d,by.x=1,by.y=1)
common_d = as.character(common_d[,1])
rd = rd1[common_d,]
ua = ua[common_d,]


############ this is what I want
> rd
a  b c
ra 15 12 9
rb 14 11 8
> ua
a b c
ra 1 3 5
rb 2 4 6


Thanks!

ben

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On Wed, Mar 07, 2012 at 09:00:14AM -0700, Ben quant
wrote:
> Hello,
> 
> I have two matrices. They both have different row names and column names,
> but they have some common row names and column names. The row names and
> column names that are the same are what I am interested in. I also want the
> columns in the two matrices aligned the same. In the end, I need to do
> rd[1,1] and ua[1,1], for example and be accessing the same column and row
> for both matrices.  Thank you very much for all you help.
> 
> I can do it, but I am pretty sure there is a better/faster way:
> 
> ################ make some sample data
> ua = matrix(c(1,2,3,4,5,6),nrow=2,ncol=3)
> colnames(ua) = c('a','b','c')
> rownames(ua)= c('ra','rb')
> rd1 = matrix(c(7,8,9,10,11,12,13,14,15,16,17,18),nrow=3,ncol=4)
> colnames(rd1) = c('c','b','a','d')
> rownames(rd1)= c('rc','rb','ra')
> 
> > rd1
> c  b  a  d
> rc 7 10 13 16
> rb 8 11 14 17
> ra 9 12 15 18
> > ua
> a b c
> ra 1 3 5
> rb 2 4 6
> 
> ##################### get common columns and rows and order them the same,
> this works but is slow'ish
> rd1_cn = colnames(rd1)
> ua_cn = colnames(ua)
> common_t = merge(rd1_cn,ua_cn,by.x=1,by.y=1)
> common_t = as.character(common_t[,1])
Hi.

Try the following instead of merge().

  common_t = intersect(rd1_cn, ua_cn)

or

  common_t = sort(intersect(rd1_cn, ua_cn))

Petr Savicky.