run_cicero: Run Cicero

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

Run Cicero

Description

A wrapper function that runs the primary functions of the Cicero pipeline with default parameters. Runs estimate_distance_parameter, generate_cicero_models and assemble_connections. See the manual pages of these functions for details about their function and parameter options. Defaults in this function are designed for mammalian data, those with non-mammalian data should read about parameters in the above functions.

Usage

run_cicero(
  cds,
  genomic_coords,
  window = 5e+05,
  silent = FALSE,
  sample_num = 100
)

Arguments

cds	Cicero CDS object, created using make_cicero_cds
genomic_coords	Either a data frame or a path (character) to a file with chromosome lengths. The file should have two columns, the first is the chromosome name (ex. "chr1") and the second is the chromosome length in base pairs. See data(human.hg19.genome) for an example. If a file, should be tab-separated and without header.
window	Size of the genomic window to query, in base pairs.
silent	Whether to print progress messages
sample_num	How many sample genomic windows to use to generate distance_parameter parameter. Default: 100.

Value

A table of co-accessibility scores

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)
  cons <- run_cicero(cicero_cds, sample_genome, sample_num = 2)

cole-trapnell-lab/cicero-release documentation built on May 11, 2023, 11:12 p.m.