run_cicero {cicero} | R Documentation

## 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)

[Package cicero version 1.5.5 Index]