Description Usage Arguments Details Value Author(s) References See Also Examples

Read the edge list of a graph from a file and construct the adjacency matrix.

1 | ```
edgelist2adj(file, vertex.names, mode = c("directed", "undirected"))
``` |

`file` |
The connection to read from. This should be a .txt file, with one edge in a line, the two vertices separated by a delimiter. |

`vertex.names` |
The names of all vertices in the graph. |

`mode` |
Whether the graph to read is directed. |

The function `edgelist2adj`

accepts a list of edges and constructs the 0-1 adjacency matrix corresponding to the graph. If `file`

contains an incomplete list of edges, the function determines the actual size of the graph through the vector `vertex.names`

.

Although named as `edgelist2adj`

, the user can also construct a 0-1 matrix corresponding to non-edges, i.e. connections that do not exist between any two vertices.

When `file`

contains incomplete information, the returned 0-1 adjacency matrix (for edges or non-edges) can be used as input in `covsel`

to estimate the complete (and weighted) adjacency matrix.

A 0-1 adjacency matrix of dimension *p \times p* corresponding to the edges defined in `file`

, where *p* is the length of the vector `vertex.names`

.

Ali Shojaie and Jing Ma

Ma, J., Shojaie, A. & Michailidis, G. (2014). Network-based pathway enrichment analysis with incomplete network information, submitted. http://arxiv.org/abs/1411.7919.

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
#Read the data
data(edgelist)
data(nonedgelist)
#Generate the .txt files
write.table(edgelist, file="edgelist.txt", row.names=FALSE)
write.table(nonedgelist, file="nonedgelist.txt", row.names=FALSE)
#Read the edge/nonedge list from files
oneMat = edgelist2adj(file="edgelist.txt", vertex.names=paste0("gene", 1:100),
mode="undirected")
zeroMat = edgelist2adj(file="nonedgelist.txt", vertex.names=paste0("gene", 1:100),
mode="undirected")
``` |

netgsa documentation built on May 30, 2017, 1:47 a.m.

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