Fit models for gene expression — fit

Fit statistical models to infer gene regulatory relationships

fit_models(
  object,
  regulators = NULL,
  targets = NULL,
  network_name = paste0(method, "_network"),
  peak_to_gene_method = c("Signac", "GREAT"),
  upstream = 1e+05,
  downstream = 0,
  extend = 1e+06,
  only_tss = FALSE,
  peak_to_gene_domains = NULL,
  gene_cor_threshold = 0.1,
  peak_cor_threshold = 0.1,
  aggregate_rna_col = NULL,
  aggregate_peaks_col = NULL,
  method = c("srm", "glm", "glmnet", "cv.glmnet", "xgb", "susie"),
  interaction_term = ":",
  adjust_method = "fdr",
  scale = FALSE,
  verbose = TRUE,
  cores = 1,
  celltype = NULL,
  ...
)

# S4 method for class 'CSNObject'
fit_models(
  object,
  regulators = NULL,
  targets = NULL,
  network_name = paste0(method, "_network"),
  peak_to_gene_method = c("Signac", "GREAT"),
  upstream = 1e+05,
  downstream = 0,
  extend = 1e+06,
  only_tss = FALSE,
  peak_to_gene_domains = NULL,
  gene_cor_threshold = 0.1,
  peak_cor_threshold = 0.1,
  aggregate_rna_col = NULL,
  aggregate_peaks_col = NULL,
  method = c("srm", "glm", "glmnet", "cv.glmnet", "xgb", "susie"),
  interaction_term = ":",
  adjust_method = "fdr",
  scale = FALSE,
  verbose = TRUE,
  cores = 1,
  celltype = NULL,
  ...
)

# S4 method for class 'matrix'
fit_models(
  object,
  regulators = NULL,
  targets = NULL,
  network_name = paste0(method, "_network"),
  peak_to_gene_method = c("Signac", "GREAT"),
  upstream = 1e+05,
  downstream = 0,
  extend = 1e+06,
  only_tss = FALSE,
  peak_to_gene_domains = NULL,
  gene_cor_threshold = 0.1,
  peak_cor_threshold = 0.1,
  aggregate_rna_col = NULL,
  aggregate_peaks_col = NULL,
  method = c("srm", "glm", "glmnet", "cv.glmnet", "xgb", "susie"),
  interaction_term = ":",
  adjust_method = "fdr",
  scale = FALSE,
  verbose = TRUE,
  cores = 1,
  celltype = NULL,
  ...
)

Arguments

object: The input data for model fitting
regulators: A character vector of regulators
targets: A character vector of target genes
network_name: Name for the inferred network
peak_to_gene_method: Method to link peaks to genes ("Signac" or "GREAT")
upstream: Distance upstream of TSS to consider
downstream: Distance downstream of TSS to consider
extend: Extension distance for GREAT method
only_tss: Whether to measure distance from TSS only
peak_to_gene_domains: Custom regulatory domains
gene_cor_threshold: Correlation threshold for TFs
peak_cor_threshold: Correlation threshold for peaks
aggregate_rna_col: Column name for RNA aggregation
aggregate_peaks_col: Column name for peaks aggregation
method: Statistical method for model fitting
interaction_term: Type of interaction variable
adjust_method: Method for p-value adjustment
scale: Whether to scale the data
verbose: Whether to show progress messages
cores: Number of cores for parallel processing
celltype: Current cell type being processed
...: Additional arguments passed to methods

Value

A list containing model coefficients and fit statistics