[BioC] how to change file format

[Adaikalavan Ramasamy]

If I understand your question, this is probably what you want.

   df <- read.delim( file="lala.txt", row.names=NULL )

This will read in a tab delimited file. If your file is comma separated
values or other formats see help(read.csv) or help(read.table). At this
point, R will automatically assign rownames from 1,2,...,8 but we can
ignore this.


   new <- paste( df[ , "Name"], df[ , "Description"], sep=" - ")
   df  <- cbind( df[ , -c(2,3)], "Name - Description"=new )

   write.table( df, file="modified_lala.txt", 
                sep="\t", quote=FALSE, row.names=FALSE )

Hopefully this should do the trick. If it does not then try changing
quote=FALSE or some other parameters.

At this point I would strongly you read help(subset) and the
Introduction to R (http://cran.r-project.org/doc/manuals/R-intro.html).

Regards, Adai



On Mon, 2005-07-25 at 22:54 -0700, weinong han wrote:
> Dear All,
>  
> My question seems not to be fit for the mail list, however, I really need your help. Crouching tigers and Hidden dragons are There!
>  
> Now ,I have the file format including 10 headers(gene, name, description, arry1,array2...array7)
> Gene Name Descriptin Array 1 Array 2 Array 3 Array 4 Array 5 Array 6 Array 7
> Gene 1 Name 1  Description 1   0.2 -0.1 -1.1 0.4 -4 -2 0.2
> Gene 2 Name 2  Description 2   2.3 2.1 -3 1.1 1.2 -1.6 0.1
> Gene 3 Name 3  Description 3   0.1 1.6 1.2 1.5 2.7 0.4 -0.4
> Gene 4 Name 4  Description 4   0.3 -1.5 -1.7 0.2 0.4 2 -2.1
> Gene 5 Name 5  Description 5   1.7 2.3 2.3 2.3 3 -2 2.1
> Gene 6 Name 6  Description 6   0.2 4 4 4 0.2 -3 -4
> Gene 7 Name 7  Description 7   -0.3 1.5 1.5 1.5 -0.2 1.7 3
> Gene 8 Name 8  Description 8   1.4 -0.6 -1.1 -0.3 -3 -3 1.4
>  
> I want to get the following file format:
>  
> 
> Gene	Name	Array 1	Array 2	Array 3	Array 4	Array 5	Array 6	Array 7Gene 1	Name 1 - Description 1	0.2	-0.1	-1.1	0.4	-4	-2	0.2Gene 2	Name 2 - Description 2	2.3	2.1	-3	1.1	1.2	-1.6	0.1Gene 3	Name 3 - Description 3	0.1	1.6	1.2	1.5	2.7	0.4	-0.4Gene 4	Name 4 - Description 4	0.3	-1.5	-1.7	0.2	0.4	2	-2.1Gene 5	Name 5 - Description 5	1.7	2.3	2.3	2.3	3	-2	2.1Gene 6	Name 6 - Description 6	0.2	4	4	4	0.2	-3	-4Gene 7	Name 7 - Description 7	-0.3	1.5	1.5	1.5	-0.2	1.7	3Gene 8	Name 8 - Description 8	1.4	-0.6	-1.1	-0.3	-3	-3	1.4
> 
> in the above file format,The first row is a header row, where the names of the 
> 
> arrays/experiments are specified from column 3 and on. The second row and on specify 
> 
> expression data for each gene, where the first column is the unique identifier of each gene, 
> 
> the second column specifies the name and the description of the gene, where the name 
> 
> and description are separated by " - " (the surrounding spaces are important), and column 3 
> 
> and on specify the expression data for the gene across all experiments.
> 
> thanks much for your help in advance
> 
> Any suggestions and advice will be much appreicated.
> 
> 
> 
> Best Regards
>  
> Han Weinong  
> hanweinong at yahoo.com
> 
> __________________________________________________
> 
> 
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