[BioC] vegan, accumulation curve
Utpal Bakshi [guest]
guest at bioconductor.org
Wed Feb 27 19:09:59 CET 2013
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
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