epoc.bootstrap {epoc}

epoc.bootstrap

Description

Bootstrap for the EPoC methods

Usage

  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)

Arguments

Y

mRNA, samples x genes.

U

CNA, samples x genes.

nboots

Number of bootstrap iterations to run.

method

For epoc.bootstrap method is "epocG" or "epocA".

x

A sparse network matrix or a list of the same, non-zeros are links. These come from e.g. epoc.final or epoc.bootstrap.

lambda.boot

The \lambdas used to run the bootstrap.

B

Number of bootstrap iterations ran for 'plot.bootsize'.

range

Range of bootstrap thresholds to display.

epocboot

For epoc.final give a list of bootstraped models from epoc.bootstrap.

k

For epoc.final and epoc.bootplot select the k sparsest model.

bthr

Require presence of links in 100*bthr% of the bootstrap iterations.

...

Parameters passed down to an underlying function. For epoc.bootstrap these are passed down to "epocG" or "epocA" respectively. For epoc.bootplot and plot.bootsize parameters are passed down to the underlying plot command.

Details

epoc.bootstrap run epocA or epocG using bootstrap.

Value

epoc.bootstrap returns a list of p \times p arrays of values in [0,1] where 1 is presence of link in 100% of bootstrap iterations for the k different \lambda values for p different genes. epoc.final returns a sparse matrix of p \times 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.

References

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)

See Also

epoc, plot.EPoC.validation, plot.EPOCA, plot.EPOCG