epoc.survival {epoc}

epoc.survival

Description

Survival analysis

Usage

  epoc.svd(model, k=1, C=1, numload=NULL)
  epoc.survival(G.svd, Y, U, surv, C=1, type=NULL)
	epoc.svdplot(G.svd, C=1)
  ## S3 method for class 'EPoC.survival'
plot(x,...)
  ## S3 method for class 'EPoC.survival'
summary(object,...)
  ## S3 method for class 'summary.EPoC.survival'
print(x,...)

Arguments

model

An object from epocG or epocA or a Matrix from epoc.bootstrap and friends.

k

In case model come from epocG or epocA select a model of sparsity level k in [1,K]. The default k=1 means first/most sparse.

C

Default 1. For epoc.svd the number of components. For epoc.survival and epoc.svdplot, which component to use.

numload

Number of loadings in the sparse components, a vector for each component. Default 10 for all components.

G.svd

The list obtained from epoc.svd.

Y

mRNA, samples x genes.

U

CNA, samples x genes.

surv

Survival data for the samples.

type

'G' means EPoC G and 'A' means EPoC A.

x

An object from epoc.survival

object

An object from epoc.survival

...

Parameters passed down to underlying functions, plot.default for plot and print.default for print.

Details

Applies survival analysis using the first SVD component, but other components can also be used by changing the input value of C. Survival scores are generated as described in Subsect. 2.4 in the second paper referenced. A simple non-parametric survival analysis is performed, comparing survival between patientswith positive or negative scores (tumor fitness).

Value

The epoc.survival object contains the summary information from a log-rank test comparing survival (survdiff) and survival fit objects.

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

Tobias Abenius, Rebecka Jörnsten, Teresia Kling, Linnéa Schmidt, José Sánchez, Sven Nelander. (2012) System-scale network modeling of cancer using EPoC. Advances in experimental medicine and biology

See Also

epoc, epoc.validation and spca