Description Usage Arguments Details Value Examples

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.

1 2 3 4 5 6 7 8 | ```
make_cicero_cds(
cds,
reduced_coordinates,
k = 50,
summary_stats = NULL,
size_factor_normalize = TRUE,
silent = FALSE
)
``` |

`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). |

`k` |
Number of cells to aggregate per bin. |

`summary_stats` |
Which numeric |

`size_factor_normalize` |
Logical, should accessibility values be normalized by size factor? |

`silent` |
Logical, should warning and info messages be printed? |

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`

Aggregated CDS object.

1 2 3 4 5 6 7 8 9 | ```
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)
``` |

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