[BioC] table values

[daphne mouzaki (RI)]

Hi Johannes and thanks for your reply.
 
The PietrLand.csv file is the file that contains the gene name, regulation (-1,1 down, up), the Breed(Pietrain=1, Landrace=2) and the Time (1,2,3,..7 which stands for 2,4,8,12,16,24,30 hours that the samples were taken respectively). Each gene was down or up regulated at different time points per breed and I want to have these info in a table. 
To be more specific :
> PL<-read.csv("PietrLand.csv",header=TRUE)
> dim(PL)
[1] 6236    4
> class(PL)
[1] "data.frame"
> PL[1:4,]
            Gene.name Regulation Breed Time
1    Ssc.7157.1.A1_at          1     1    1
2    Ssc.9062.1.A1_at          1     1    1
3 Ssc.14467.2.S1_a_at          1     1    1
4   Ssc.19413.1.A1_at          1     1    1
> q<-table(PL[,c(1,4)]) 
> dim(q)
[1] 2568    7
> q[1:4,]
                     Time
Gene.name             1 2 3 4 5 6 7
  AFFX-Ss_IRP_3_at    1 1 2 0 0 1 1
  AFFX-Ss_IRP_5_at    0 0 1 0 0 0 0
  AFFX-Ss_IRP_M_at    0 0 1 0 0 0 0
  AFFX-SSC-28SrRNA_at 0 0 1 0 1 1 0

What I would like to have is a combination of Time-Breed information per gene. As you can notice
at different time points genes are differentially expressed ( up-down regulated) and I want to keep track of the gene behaviour per breed. More specifically sth like this :
                     
Gene.name                     Breed1                                    Breed 2
                                      Time min Time max                 Time min  Time max
  AFFX-Ss_IRP_3_at        2            4                              2             5
  AFFX-Ss_IRP_5_at        1            6                              3             7
This info mean for example the first gene that the gene was appearing down regulated at time point 2 and up regulated for time 4 for the first breed and that the gene was appearing down reg. at time point 2 and up regulated for time point 5 for the second breed.  The resulting table should have 2568 X 4 dimensions. I thought about using the function apply() but it needs a matrix and this is not a matrix. 
 
Cheers,
Daphne