R help - May 2012 - data conversion (possibly with reshape package)

Hi everyone,

I have an issue with a data conversion. First, I tried it with the
reshape-package, but since it's quite a while that I used it, I feel kind
of rusty...

I have a data.frame like this:

 id          Sample.Name               Marker           Allele.1
Allele.2            sample_id            species
1            01_primer01                  Dalb01           165
     179                  SH233             D. madagascariensis
2            01_primer04                  Dalb04            221
    225                  SH233             D. madagascariensis
3            01_primer08                  Dalb08            218
    218                  SH233             D. madagascariensis
4            01_primer10                  Dalb10            134
    134                  SH233             D. madagascariensis
5            01_primer14                  Dalb14            250
    250                  SH233             D. madagascariensis
6            01_primer16                  Dalb16            232
    232                  SH233             D. madagascariensis


this was just the head(), in fact, the sample_id col has different ids, I
would like to aggregate matching sample_id's into one
and would like to get something like this:

species                           sample_id             Marker1_Allele1
     Marker1_Allele2          Marker2_Allele1          Marker2_Allele2
...   Marker31_Allele1      Marker31_Allele2

D. madagascariensis       SH233                 179
            225                                  134
   244                             308                     322
D. baronii                        SH151                 123
                    134                                  155
           155                             307                     312


I tried to prepare the cast() but didn't quite figure out how to achieve
this.  I tried to first merge with the following:

                genMelt <- melt(geno, id = c(1:2, 5:6))

then I created a column:

               genMelt$Locus <- substring(as.character(genMelt$Panel),5, 6)

               genMelt$Locus <- paste(genMelt$Locus, genMelt$variable, sep
= "_")

So I get a column in the appropriate format. But when I cast :

               mycast <- cast(genMelt,sample_id~Locus)

I get just the frequencies of the Loci per sample_id


Maybe I don't even need reshape, I also thought about a loop. If you have
any idea on this, I appreciate it

Cheers,
Martin

	[[alternative HTML version deleted]]