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Srinivas Iyyer

2006-Jul-06 12:18 UTC

[R] Comparing two matrices

hi:

I have matrix with dimensions(200 X 20,000). I have
another file, a tab-delim file where first column
variables are row names and second column variables
are column names. 


For instance:
> tmat  Apple Orange Mango Grape Star
A     0      0     0     0    0
O     0      0     0     0    0
M     0      0     0     0    0
G     0      0     0     0    0
S     0      0     0     0    0


> tb # tab- delim file.       V1 V2
1  Apple  S
2  Apple  A
3  Apple  O
4 Orange  A
5 Orange  O
6 Orange  S
7  Mango  M
8  Mango  A
9  Mango  S


I have to read each line of the 'tb' (tab delim file),
take the first variable, check if matches any rowname
of the matrix. Take the second variable of the row in
and check if it matches any column name.  If so,  put
1 else leave it. 


The following is a small piece of code that, I felt is
a solutions. However, since my original matrix and
tab-delim file is very very huge, I am not sure if it
is really doing the correct thing. Could any one
please help me if I am doing this correct. 


> for(i in 1:length(tb[,1])){+  r = tb[i,1]
+  c = as.character(tb[i,2])
+  tmat[rownames(tmat)==c,colnames(tmat)==r] <-1
+ }


> tmat  Apple Orange Mango Grape Star
A     1      1     1     0    0
O     1      1     0     0    0
M     0      0     1     0    0
G     0      0     0     0    0
S     1      1     1     0    0



Thanks.

Peter Dalgaard

2006-Jul-06 12:37 UTC

head link

[R] Comparing two matrices

Srinivas Iyyer <srini_iyyer_bio at yahoo.com> writes:
> hi:
> 
> I have matrix with dimensions(200 X 20,000). I have
> another file, a tab-delim file where first column
> variables are row names and second column variables
> are column names. 
> 
> 
> For instance:
> 
> > tmat
>   Apple Orange Mango Grape Star
> A     0      0     0     0    0
> O     0      0     0     0    0
> M     0      0     0     0    0
> G     0      0     0     0    0
> S     0      0     0     0    0
> 
> 
> 
> > tb # tab- delim file. 
>       V1 V2
> 1  Apple  S
> 2  Apple  A
> 3  Apple  O
> 4 Orange  A
> 5 Orange  O
> 6 Orange  S
> 7  Mango  M
> 8  Mango  A
> 9  Mango  S
> 
> 
> I have to read each line of the 'tb' (tab delim file),
> take the first variable, check if matches any rowname
> of the matrix. Take the second variable of the row in
> and check if it matches any column name.  If so,  put
> 1 else leave it. 
> 
> 
> The following is a small piece of code that, I felt is
> a solutions. However, since my original matrix and
> tab-delim file is very very huge, I am not sure if it
> is really doing the correct thing. Could any one
> please help me if I am doing this correct. 
> 
> 
> 
> > for(i in 1:length(tb[,1])){
> +  r = tb[i,1]
> +  c = as.character(tb[i,2])
> +  tmat[rownames(tmat)==c,colnames(tmat)==r] <-1
> + }
There are much faster ways. Try (untested)

n1 <- match(tb$V1, rownames(tmat))
n2 <- match(tb$V2, colnames(tmat))
m <- unique(cbind(n1,n2)[complete.cases(n1,n2),])
tmat[m] <- 1

The unique() part may or may not be beneficial. 



-- 
   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

Dimitris Rizopoulos

2006-Jul-06 12:43 UTC

head link

[R] Comparing two matrices

try something like:

mat1 <- matrix(0, 26, 100, dimnames = list(letters, 1:100))
mat2 <- cbind(sample(letters, 10), sample(100, 10))
###########
mat1[cbind(match(mat2[, 1], rownames(mat1)), match(mat2[, 2], 
colnames(mat1)))] <- 1


I hope it helps.

Best,
Dimitris

----
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
     http://www.student.kuleuven.be/~m0390867/dimitris.htm


----- Original Message ----- 
From: "Srinivas Iyyer" <srini_iyyer_bio at yahoo.com>
To: <r-help at stat.math.ethz.ch>
Sent: Thursday, July 06, 2006 2:18 PM
Subject: [R] Comparing two matrices

> hi:
>
> I have matrix with dimensions(200 X 20,000). I have
> another file, a tab-delim file where first column
> variables are row names and second column variables
> are column names.
>
>
> For instance:
>
>> tmat
>  Apple Orange Mango Grape Star
> A     0      0     0     0    0
> O     0      0     0     0    0
> M     0      0     0     0    0
> G     0      0     0     0    0
> S     0      0     0     0    0
>
>
>
>> tb # tab- delim file.
>      V1 V2
> 1  Apple  S
> 2  Apple  A
> 3  Apple  O
> 4 Orange  A
> 5 Orange  O
> 6 Orange  S
> 7  Mango  M
> 8  Mango  A
> 9  Mango  S
>
>
> I have to read each line of the 'tb' (tab delim file),
> take the first variable, check if matches any rowname
> of the matrix. Take the second variable of the row in
> and check if it matches any column name.  If so,  put
> 1 else leave it.
>
>
> The following is a small piece of code that, I felt is
> a solutions. However, since my original matrix and
> tab-delim file is very very huge, I am not sure if it
> is really doing the correct thing. Could any one
> please help me if I am doing this correct.
>
>
>
>> for(i in 1:length(tb[,1])){
> +  r = tb[i,1]
> +  c = as.character(tb[i,2])
> +  tmat[rownames(tmat)==c,colnames(tmat)==r] <-1
> + }
>
>
>
>> tmat
>  Apple Orange Mango Grape Star
> A     1      1     1     0    0
> O     1      1     0     0    0
> M     0      0     1     0    0
> G     0      0     0     0    0
> S     1      1     1     0    0
>
>
>
> Thanks.
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
> 

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Duncan Murdoch

2006-Jul-06 12:46 UTC

head link

[R] Comparing two matrices

On 7/6/2006 8:18 AM, Srinivas Iyyer wrote:> hi:
> 
> I have matrix with dimensions(200 X 20,000). I have
> another file, a tab-delim file where first column
> variables are row names and second column variables
> are column names. 
> 
> 
> For instance:
> 
>> tmat
>   Apple Orange Mango Grape Star
> A     0      0     0     0    0
> O     0      0     0     0    0
> M     0      0     0     0    0
> G     0      0     0     0    0
> S     0      0     0     0    0
> 
> 
> 
>> tb # tab- delim file. 
>       V1 V2
> 1  Apple  S
> 2  Apple  A
> 3  Apple  O
> 4 Orange  A
> 5 Orange  O
> 6 Orange  S
> 7  Mango  M
> 8  Mango  A
> 9  Mango  S
> 
> 
> I have to read each line of the 'tb' (tab delim file),
> take the first variable, check if matches any rowname
> of the matrix. Take the second variable of the row in
> and check if it matches any column name.  If so,  put
> 1 else leave it. 
> 
> 
> The following is a small piece of code that, I felt is
> a solutions. However, since my original matrix and
> tab-delim file is very very huge, I am not sure if it
> is really doing the correct thing. Could any one
> please help me if I am doing this correct. 
> 
> 
> 
>> for(i in 1:length(tb[,1])){
> +  r = tb[i,1]
> +  c = as.character(tb[i,2])
> +  tmat[rownames(tmat)==c,colnames(tmat)==r] <-1
> + }
I think that works, but it's not as fast as some other ways of doing the 
same thing.  For example, table(tb) will give you a table of the counts 
of each pair of entries in tb.  pmin(table(tb), 1) will set the maximum 
count to 1.

An advantage of this approach is that it will show you if there are any 
entries in tb that aren't in your tmat (typos, etc.).  A disadvantage is 
that if there are any missing categories (e.g. G, Grape, Star in your 
sample) they won't show up at all, and you may need some manipulations 
to get things to look exactly the way you asked.  For example,

 > pmin(table(tb))
         V2
V1       A M O S
   Apple  1 0 1 1
   Mango  1 1 0 1
   Orange 1 0 1 1
 > pmin(table(tb[,2:1]))
    V1
V2  Apple Mango Orange
   A     1     1      1
   M     0     1      0
   O     1     0      1
   S     1     1      1


Duncan Murdoch


> 
> 
> 
>> tmat
>   Apple Orange Mango Grape Star
> A     1      1     1     0    0
> O     1      1     0     0    0
> M     0      0     1     0    0
> G     0      0     0     0    0
> S     1      1     1     0    0
> 
> 
> 
> Thanks.
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

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