Description Usage Arguments Details Value References See Also
Bootstrap for the EPoC methods
1 2 3 4 | epoc.bootstrap(Y, U, nboots=100, bthr=NULL, method='epocG',...)
## S3 method for class 'bootsize'
plot(x, lambda.boot=NULL, B, range=c(0,1), ...)
epoc.final(epocboot, bthr=0.2, k)
|
Y |
mRNA, samples x genes. |
U |
CNA, samples x genes. |
nboots |
Number of bootstrap iterations to run. |
method |
For |
x |
A sparse network matrix or a list of the same, non-zeros are links. These come from e.g. |
lambda.boot |
The λs used to run the bootstrap. |
B |
Number of bootstrap iterations ran for |
range |
Range of bootstrap thresholds to display. |
epocboot |
For |
k |
For |
bthr |
Require presence of links in 100*bthr% of the bootstrap iterations. |
... |
Parameters passed down to an underlying function. For |
epoc.bootstrap
run epocA
or epocG
using bootstrap.
epoc.bootstrap
returns a list of p x p arrays of values in [0,1] where 1 is presence of link in 100% of bootstrap iterations for the k different λ values for p different genes.
epoc.final
returns a sparse matrix of p x p values in [0,1] where 1 is presence of link in 100% of bootstrap iterations, but thresholded such that all values have be greater than or equal to bthr
.
Rebecka Jörnsten, Tobias Abenius, Teresia Kling, Linnéa Schmidt, Erik Johansson, Torbjörn Nordling, Bodil Nordlander, Chris Sander, Peter Gennemark, Keiko Funa, Björn Nilsson, Linda Lindahl, Sven Nelander. (2011) Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Molecular Systems Biology 7 (to appear)
epoc
, plot.EPoC.validation
, plot.EPOCA
, plot.EPOCG
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