Hi!
I'm new in R and I'm writing you asking for some guidance. I had
analyzed a comparative genomic microarray data of /56 Salmonella/
strains to identify absent genes in each of the serovars, and finally I
got a matrix that looks like that:
> data[1:5,1:5]
Abortusovis07918 Agona08561 Anatum08125 Arizonae65S Braenderup08488
1 S5305B_IGR S5305B_IGR S5305B_IGR S5305B_IGR S5305B_IGR
2 S5305A_IGR S5300A_IGR S5305A_IGR S5300A_IGR S5300A_IGR
3 S5300A_IGR S5300B_IGR S5300A_IGR S5300B_IGR S5300B_IGR
4 S5300B_IGR S5299B_IGR S5300B_IGR S5299B_IGR S5299B_IGR
5 S5299B_IGR S5299A_IGR S5299B_IGR S5829B_IGR S5299A_IGR
The variables corresponds to those genes identified as absent in each of
the serovars. I would like to create a presence-absence matrix of those
genes comparing all the serovars at the same time, I assume that should
not be complicated but I don't know how to do it.
I would like a matrix similar to the next one:
> data_m[1:5,1:5]
Abortusovis07918 Agona08561 Anatum08125 Arizonae65S
Braenderup08488
S5305B_IGR 1 1 1 1 1
S5305A_IGR 1 0 1 0 0
S5300A_IGR 1 1 1 1 1
Any help would be welcome, and thank you in advance,
Oihane
--
Oihane Irazoki Sanchez
PhD Student, Molecular Microbiology
Genetics and Microbiology Department, Faculty of Biosciences
Autonomous University of Barcelona
08193 Bellaterra (Barcelona), Spain
Telf: 34 - 935 811 665
E-mail: oihane.iraz...@uab.cat / o.iraz...@gmail.com
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