make_cicero_cds {cicero} | R Documentation

## Create cicero input CDS

### Description

Function to generate an aggregated input CDS for cicero. `run_cicero` takes as input an aggregated cicero CDS object. This function will generate the CDS given an input CDS (perhaps generated by `make_atac_cds`) and a value for k, which is the number of cells to be aggregated per bin. The default value for k is 50.

### Usage

    make_cicero_cds(cds, reduced_coordinates, k = 50, summary_stats = NULL,
      size_factor_normalize = TRUE, silent = FALSE)

### Arguments

`cds` | Input CDS object.
`reduced_coordinates` | A data frame with columns representing the coordinates of each cell in reduced dimension space (generally 2-3 dimensions). `row.names(reduced_coordinates)` should match the cell names in the CDS object. If dimension reduction was done using monocle, tSNE coordinates can be accessed by `t(reducedDimA(cds))`, and DDRTree coordinates can be accessed by `t(reducedDimS(cds))`.
`k` | Number of cells to aggregate per bin.
`summary_stats` | Which numeric `pData(cds)` columns you would like summarized (mean) by bin in the resulting CDS object.
`size_factor_normalize` | Logical, should accessibility values be normalized by size factor?
`silent` | Logical, should warning and info messages be printed?

### Details

Aggregation of similar cells is done using a k-nearest-neighbors graph and a randomized "bagging" procedure. Details are available in the publication that accompanies this package. Run `citation("cicero")` for publication details. KNN is calculated using `knn.index`

### Value

Aggregated CDS object.

### Examples

      data("cicero_data")

      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)

[Package cicero version 1.2.0 Index]