Hi Carlos,

how about this step first:

rownames(mydata)<-gsub("361a","00361a",rownames(mydata))
rownames(mydata)<-gsub("456a","00456a",rownames(mydata))

good luck

milton
On Thu, Aug 27, 2009 at 12:27 PM, Carlos Gonzalo Merino Mendez <
carlosgmer...@yahoo.com> wrote:

> Hello everyone, I would appreciate any help with the following.
>
> My dataset is a list containing matrices. So if you type e.g.
>
> data[[1]]
>
> you get something like:
>
>           [,1]    [,2]
> 361a       A    T
> 456b       A    G
> 72145a    T    G
> ........
>
> As you can see my rows have names which are character strings containing
> numbers and letters. I want something similar to a histogram, per column.
> i.e. I want to know how many times I have a single repeat character in a
> column and how many times I have a twice repeated character and so on. Maybe
> there is an easy way to do this, but I wrote my own code which works
> perfectly, so don't bother to correct it unless extremely necessary. I write
> down the code so you know exactly what I'm trying to do:
>
> table <- vector()
>
> for (i in (1:length(data))){
>
>    for (j in (1:length(data[[i]][1,]))){
>
>        t <- table(data[[i]][,j])
>
>        table <- c(table, t)
> }}
>
> ncount <- table[names(table) != "-"] #this line is necessary to eliminate
> "-" characters which should not be included in the analysis
>
> sfs <- table (ncount)
>
> And with this code I get something like:
>
>  1   2   3   4   5   6   7   8   9  10 ....
>
> 542 125  98  49  47  41  26  31  22  18  ....
>
> which is what I'm looking for.
>
>
> Now comes THE problem:
>
> As I said before my rows have names. Each name is unique. I want to apply
> my analysis to a subset of rows en each matrix, namely all rows whose names
> start with 3, all that start with 4, all that start with 721. In most cases
> only the first character is important, but since I have names of different
> length, in some cases I need the first three characters to differentiate the
> groups. I want to integrate this into the loop so that I get a vector (such
> as the one called "table" in my code) for each subset analyzed.
>
> I tried using the subset function, but I couldn't figure out how to use it,
> because it's intended to use row values to define the subset, not row names.
>
> I hope someone can help me out, but please bear in mind I am really new at
> R and most commands and parameters are really unfamiliar to me.
>
> Thanks.
>
>
>
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>
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>

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