[BioC] vegan, accumulation curve

[Utpal Bakshi [guest]]

Hi,

Any one have any idea about core genomic accumulation curve from the orthomcl output file?? 

My modified orthomcl output file looks something like:

Gr1 Gr2 Gr3 Gr4                     ..............
row1 1 1 1 0                          ..............
row2 0 1 0 1                           ...............
row3 1 1 0 1   
                         ..............
...................
.................

from this file, I determine the pan genomic (total file as input) accumulation curve from the speccecum function of vegan as: 

mydata <- read.table('input_matrix_file.txt')
sp <- specaccum(mydata, "random", permutations="100")

But the problem I face is in determining core gene accumulation (rather depletion) curve (permutations of only 1-1 combinations) from this file. I could not find a way of doing it from this matrix file. 

I will be grateful if you anyone offer some advice to solve this problem.
Thanks for your consideration.

Utpal Bakshi


 -- output of sessionInfo(): 

R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] vegan_2.0-2   permute_0.6-2

loaded via a namespace (and not attached):
[1] grid_2.13.1     lattice_0.19-30


--
Sent via the guest posting facility at bioconductor.org.