R help - Jul 2006 - String frequencies in rows

Hi All,
 
I’m trying to evaluate the frequency of different strings in each row of a
data.frame :
INPUT:
ID G1 G2 G3 G4 … GN
1 AA BB AB AB … 
2 BB AB AB AA … 
3 AC CC AC AA … 
4  BB BB BB BB… 

The number of different strings can vary in each row.
 
My solution has been:
for (i in 1:length(INPUT[,1])){
 b=as.data.frame(table(t((INPUT[i,2:5]))))
<some operations using the string values and frequencies>
(e.g. b for i==1 is:
 AA 1
 BB 1
 AB 2 )
} 

However my dataframe contains thousands rows and this script takes a lot of
time.
Could someone suggest me a faster way?
 
Thank you very much,
Mario Falchi
	[[alternative HTML version deleted]]

Mario Falchi <mariofalchi <at> yahoo.com> writes:
> I???m trying to evaluate the frequency of different strings in each row of
a
data.frame :
> INPUT:
> ID G1 G2 G3 G4 ??? GN
> 1 AA BB AB AB ??? 
  Something like

z <- data[,-1]
table(z,row(z))

  ?

  Ben Bolker

It's usually faster to operate on columns of data frames, rather
than rows, so the following might help:

R> x
  G1 G2 G3 G4
1 AA BB AB AB
2 BB AB AB AA
3 AC CC AC AA
4 BB BB BB BB
R> xt <- as.data.frame(t(x))
R> sapply(xt, table)
$`1`

AA AB BB 
 1  2  1 

$`2`

AA AB BB 
 1  2  1 

$`3`

AA AC CC 
 1  2  1 

$`4`

BB 
 4 

Andy 

From: Mario Falchi
> 
> Hi All,
>  
> I???m trying to evaluate the frequency of different strings 
> in each row of a data.frame :
> INPUT:
> ID G1 G2 G3 G4 ??? GN
> 1 AA BB AB AB ???
> 2 BB AB AB AA ???
> 3 AC CC AC AA ???
> 4  BB BB BB BB??? 
> 
> The number of different strings can vary in each row.
>  
> My solution has been:
> for (i in 1:length(INPUT[,1])){
>  b=as.data.frame(table(t((INPUT[i,2:5]))))
> <some operations using the string values and frequencies> 
> (e.g. b for i==1 is:
>  AA 1
>  BB 1
>  AB 2 )
> } 
> 
> However my dataframe contains thousands rows and this script 
> takes a lot of time.
> Could someone suggest me a faster way?
>  
> Thank you very much,
> Mario Falchi
> 	[[alternative HTML version deleted]]
> 
>