assemble_connections: Combine and reconcile cicero models

In cole-trapnell-lab/cicero: Predict cis-co-accessibility from single-cell chromatin accessibility data

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)

cole-trapnell-lab/cicero documentation built on March 13, 2023, 6:02 p.m.