assemble_connections {cicero} | R Documentation

## Combine and reconcile cicero models

### Description

Function which takes the output of `generate_cicero_models` and assembles the connections into a data frame with cicero co-accessibility scores.

### Usage

    assemble_connections(cicero_model_list, silent = FALSE)

### Arguments

`cicero_model_list` | A list of cicero output objects, generally, the output of `generate_cicero_models`.
`silent` | Logical, should the function run silently?

### Details

This function combines glasso models computed on overlapping windows of the genome. Pairs of sites whose regularized correlation was calculated twice are first checked for qualitative concordance (both zero, positive or negative). If they not concordant, NA is returned. If they are concordant the mean is returned.

### Value

A data frame of connections with their cicero co-accessibility scores.

### See Also

`generate_cicero_models`

### Examples

      data("cicero_data")
      data("human.hg19.genome")
      sample_genome <- subset(human.hg19.genome, V1 == "chr18")
      sample_genome$V2[1] <- 100000
      input_cds <- make_atac_cds(cicero_data, binarize = TRUE)
      input_cds <- reduceDimension(input_cds, max_components = 2, num_dim=6,
                                   reduction_method = 'tSNE',
                                   norm_method = "none")
      tsne_coords <- t(reducedDimA(input_cds))
      row.names(tsne_coords) <- row.names(pData(input_cds))
      cicero_cds <- make_cicero_cds(input_cds, reduced_coordinates = tsne_coords)
      model_output <- generate_cicero_models(cicero_cds,
                                             distance_parameter = 0.3,
                                             genomic_coords = sample_genome)
      cicero_cons <- assemble_connections(model_output)

[Package cicero version 1.5.5 Index]