Generate aggregated inputs for the SCEG-HiC model using the
Aggregate_datasets function.
Usage
Aggregate_datasets(
object,
k_neigh = 50,
rna_assay = "RNA",
atac_assay = "peaks",
cellnames = NULL,
atacbinary = TRUE,
max_overlap = 0.8,
reduction.name = NULL,
size_factor_normalize = TRUE,
seed = 123,
verbose = TRUE
)Arguments
- object
A Seurat object.
- k_neigh
Integer. Number of cells to aggregate per group (default is 50).
- rna_assay
Character. Name of the assay containing gene expression data.
- atac_assay
Character. Name of the assay containing peak (chromatin accessibility) data.
- cellnames
Character vector. Name(s) of one or more metadata columns used to group the cells. Default is the current cell identities.
- atacbinary
Logical. Should the aggregated scATAC-seq matrix be binarized?
- max_overlap
Numeric. Maximum allowed overlap ratio between two aggregated groups (default is 0.8).
- reduction.name
Character. Name of the dimensionality reduction to use for extracting cell coordinates for aggregation.
- size_factor_normalize
Logical. Whether to normalize accessibility values using size factors.
- seed
Integer. Random seed.
- verbose
Logical. Should progress messages and warnings be printed?