Description Usage Arguments Value Author(s) Examples

View source: R/interaction-methods.R

Count the number of genetic interactions within and between the elements of the interactome.

1 | ```
getInteraction(iMat, universe, interactome)
``` |

`iMat` |
Interaction matrix. Each entry has value 0 or 1, representing positive or negative interaction of corresponding pairs of row and column, respectively. |

`universe` |
Character vector of gene names, e.g., array genes used in synthetic genetic array experiments (SGA) |

`interactome` |
Adjacency matrix where row are gene names and columns are cellular organizational units. |

The returned value is a list of 2 matrices:

`bwMat` |
A interaction matrix that corresponds to the cellular organizational units interaction matrix where row and columns a organizational units names and the value inside the matrix are the number of genetic interactions they share. |

`CDs` |
Subset of the input interactome that shares interactions. |

N. LeMeur

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
##Create the genetic interaction matrix
gInt <- sample(c(0, 1), 25, TRUE)
iMat <- matrix(gInt, nrow=5, ncol=5, dimnames=list(letters[1:5],letters[4:8]))
##Create the interactome
cInt <- sample(c(0,1),30, TRUE)
interactome <- matrix(cInt, nrow=6, ncol=5,dimnames=list(letters[2:7],LETTERS[1:5]))
## Reduce the genetic interaction matrix to match the gene present in
## the interactome
reducediMat <- gi2Interactome(iMat, interactome)
## Get the interaction
prey <- letters[1:20]
myInteraction <- getInteraction(reducediMat, prey, interactome)
``` |

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