[R] Counting variables repeted in dataframe columns to create a presence-absence table

[arun]

Hi,
Try:
data_m <- read.table(text="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",sep="",header=TRUE,stringsAsFactors=FALSE)
 data_m$new <-1
library(reshape2)
 dM <- melt(data_m,id.vars="new")
xtabs(new~value+variable,dM)
#or
 dcast(dM,value~variable,value.var="new",fill=0)


A.K.


On Thursday, November 28, 2013 12:18 PM, Gmail <o.irazoki at gmail.com> wrote:
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.irazoki at uab.cat / o.irazoki at gmail.com


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