R help - Jan 2010 - Remove part of string in colname and calculate mean for columns groups

Hi all,

 

I have two question. First, I wonder how to remove a part of the column names in
a matrix? I would like to remove the "_ACCX" or "_NAX" part
below. Is there a method where the "_" as well as all characters after
i can be removed?

 
> dim(exprdata)
[1]  88 512
>
> colnames(exprdata[,c(1:20)])
 [1] "Akita_ACC1" "Akita_ACC2" "Akita_ACC3"
"Akita_ACC4" "Alc.0_ACC1" "Alc.0_ACC2"
"Alc.0_ACC3"
 [8] "Alc.0_ACC4" "Alc.0_ACC5" "Bl.1_ACC1" 
"Bl.1_ACC2"  "Bl.1_ACC3"  "Bl.1_ACC4" 
"Bla.1_ACC1"
[15] "Bla.1_ACC2" "Bla.1_ACC3" "Bla.1_ACC4"
"Blh.1_ACC1" "Blh.1_ACC2" "Blh.1_ACC3"

 

 

Secondly, I would like to calculate the mean of each column group in the matrix,
for instance all columns beginning with "Akita", and save all new
columns as a new matrix.

 

For instance, use:

 
> head(exprdata[,c(1:4)])
            Akita_ACC1 Akita_ACC2 Akita_ACC3 Akita_ACC4
A100005-101   6.668931         NA         NA         NA
A122001-101  10.562564  11.706395  11.608989   8.289093
A128001-101  14.946749   8.112625   8.176438  10.104254
A133001-101   5.186679   6.089870   4.119589   3.168841
A133003-101         NA         NA  19.825480   2.587695
A134001-101   3.259402   4.835642   4.679607   4.490254

 

To get something like:

 

                         Akita
A100005-101   6.668931    

A122001-101   10.54176  

A128001-101  10.10425
A133001-101   3.168841

A133003-101   2.587695 
A134001-101   4.490254

 

 

However, the column groups are of different sizes (3-10 columns) so I guess
I'll need a method based on the column names.

 

Anyone who can help me?

 

Best regards,

 

Joel
 		 	   		  
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Joel F?rstenberg-H?gg wrote:
> 
> 
> 
> I have two question. First, I wonder how to remove a part of the column
> names in a matrix? I would like to remove the "_ACCX" or
"_NAX" part
> below. Is there a method where the "_" as well as all characters
after i
> can be removed?
> 
> Secondly, I would like to calculate the mean of each column group in the
> matrix, for instance all columns beginning with "Akita", and save
all new
> columns as a new matrix. 
>  
> 
If you do that in the example you gave, duplicate column names would be the
result, but let's assume that was a typo.

# Simplify names
data = data.frame(Akita.0_ACC1=1:2,Akita.1_ACC2=2:3,Alc.0_ACC1=3:4)
names(data) = sub("_.*","",names(data))
# Make a new data frame with the Akitas only
dataAkita = data[,grep("Akita",names(data))]

To do the averaging, check the examples in package plyr. 

Dieter






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