Description Usage Arguments Author(s) References See Also Examples

View source: R/pathwayFunctions.R

Plotting the topology of a pathway's regulatory network as reconstructed from from DNA copy number and gene expression data by the `pathway1sample`

-function.

1 2 | ```
pathwayPlot(pFit, directed = TRUE, tWidth = 1, cWidth = 1, geWidth=10,
cnWidth=10, circleDist = 1.5, gNames = NULL, main = "", remove = FALSE)
``` |

`pFit` |
Object of class |

`directed` |
A |

`tWidth` |
A |

`cWidth` |
A |

`geWidth` |
A |

`cnWidth` |
A |

`circleDist` |
A |

`gNames` |
A |

`main` |
The |

`remove` |
A |

Wessel N. van Wieringen: [email protected]

Van Wieringen, W.N., Van de Wiel, M.A. (2012), "Modeling the *cis*- and *trans*-effect of DNA copy number aberrations on gene expression levels in a pathway", *submitted for publication*.

See also `pathway1sample`

.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ```
# set number of genes (p) and samples (n)
p <- 10
n <- 1000
# sample cis-effects
beta <- abs(rnorm(p))
# sample trans-effects
Theta <- matrix(sample(c(-1,1), p^2, replace=TRUE, prob=c(0.2, 0.8)), ncol=p) *
matrix(runif(p^2), ncol=p) / 4
diag(Theta) <- 1
# sample error variances
Sigma <- diag(rchisq(p, df=1)/5 + 0.5)
# sample DNA copy number data
X <- matrix(runif(n*p, min=-2, max=2), ncol=p)
# sample gene expression data
Y <- t(apply(X, 1, function(Y, beta){ Y * beta }, beta=beta)) %*% t(solve(Theta)) +
rmvnorm(n, sigma=solve(Theta) %*% Sigma %*% t(solve(Theta)))
# fit model
pFit <- pathway1sample(Y, X, lambda1=500)
# plot pathway topology
pathwayPlot(pFit, tWidth=5, cWidth=5)
``` |

```
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: CGHbase
Loading required package: marray
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: mvtnorm
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```

sigaR documentation built on May 6, 2019, 3:40 a.m.

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