infer_grn | R Documentation |
Pando
Infer a Gene Regulatory Network with Pando
infer_grn(object, ...)
## S3 method for class 'GRNData'
infer_grn(
object,
genes = NULL,
network_name = paste0(method, "_network"),
peak_to_gene_method = c("Signac", "GREAT"),
upstream = 1e+05,
downstream = 0,
extend = 1e+06,
only_tss = FALSE,
parallel = FALSE,
tf_cor = 0.1,
peak_cor = 0,
aggregate_rna_col = NULL,
aggregate_peaks_col = NULL,
method = c("glm", "glmnet", "cv.glmnet", "brms", "xgb", "bagging_ridge",
"bayesian_ridge"),
alpha = 0.5,
family = "gaussian",
interaction_term = ":",
adjust_method = "fdr",
scale = FALSE,
verbose = TRUE,
...
)
... |
Other parameters for the model fitting function. |
genes |
A character vector with the target genes to consider for GRN inference. Takes all VariableFeatures in the object per default. |
peak_to_gene_method |
Character specifying the method to link peak overlapping motif regions to nearby genes. One of 'Signac' or 'GREAT'. |
upstream |
Integer defining the distance upstream of the gene to consider as potential regulatory region. |
downstream |
Integer defining the distance downstream of the gene to consider as potential regulatory region. |
extend |
Integer defining the distance from the upstream and downstream of the basal regulatory region.
Only used of |
only_tss |
Logical. Measure distance from the TSS ( |
parallel |
Logical. Whether to parallelize the computation with |
tf_cor |
Threshold for TF - target gene correlation. |
peak_cor |
Threshold for binding peak - target gene correlation. |
method |
A character string indicating the method to fit the model.
|
alpha |
The elasticnet mixing parameter. See |
family |
A description of the error distribution and link function to be used in the model.
See |
interaction_term |
The interaction term to use in the model between TF and binding site.
|
adjust_method |
Method for adjusting p-values. |
scale |
Logical. Whether to z-transform the expression and accessibility matrices. |
verbose |
Logical. Display messages. Set verbose to '2' to print errors for all model fits. |
A GRNData object.
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