assemble_connections: Combine and reconcile cicero models

Description Usage Arguments Details Value See Also Examples

View source: R/runCicero.R

Description

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

Usage

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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

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  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)

cicero documentation built on Dec. 7, 2018, 6 p.m.