Description Usage Arguments Value Author(s) Examples

Infer gene co-expression networks

1 | ```
sclink_net(expr, ncores, lda = seq(1, 0.1, -0.05), nthre = 20, dthre = 0.9)
``` |

`expr` |
A gene expression matrix with rows representing cells and columns representing genes.
Gene names are given as column names. Can be the output of |

`ncores` |
Number of cores if using parallel computation. |

`lda` |
A vector specifying a sequence of lambda values to be used in the penalized likelihood. |

`nthre` |
An integer specifying a threshold on the number of complete observations. Defaults to 20. |

`dthre` |
A number specifying the threshold on dropout probabilities. Defaults to 0.9. |

A list for gene co-expression relationships. The list contains a `cor`

element for
scLink's correlation matrix and a `summary`

element for the gene networks. `summary`

is a list
with each element corresponding to the result of one lambda value. Each element of `summary`

contains the following information:

- adj:
the adjacency matrix specifying the gene-gene edges;

- Sigma:
the estimated concentration matrix;

- nedge:
number of edges in the gene network;

- bic:
BIC score;

- lambda:
value of lambda in the penalty.

Wei Vivian Li, vivian.li@rutgers.edu

1 2 3 | ```
count = readRDS(system.file("extdata", "example.rds", package = "scLink"))
count.norm = sclink_norm(count, scale.factor = 1e6, filter.genes = TRUE, n = 500)
networks = sclink_net(expr = count.norm, ncores = 1, lda = seq(0.5, 0.1, -0.05))
``` |

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