Define target genes from hummus object
define_target_genes.RdCalling the define_output function with output_type = 'target_genes'
Usage
define_target_genes(
hummus_object,
multiplex_names = NULL,
bipartites_names = NULL,
config_name = "target_genes_config.yml",
config_folder = "config",
tf_multiplex = "TF",
atac_multiplex = "peaks",
rna_multiplex = "RNA",
multilayer_f = "multilayer",
gene_list = NULL,
tf_list = NULL,
save = FALSE,
output_f = NULL,
return_df = TRUE,
suffix_bipartites = ".tsv",
njobs = 1
)Arguments
- hummus_object
A hummus object
- multiplex_names
A vector of multiplex names considered. It must be a subset of the names of the multiplexes in the hummus object.
- bipartites_names
A vector of bipartites names considered. It must be a subset of the names of the bipartites in the hummus object.
- config_name
The name of the config file to be created by hummuspy
- config_folder
The folder where the config file will be created
- tf_multiplex
The name of the multiplex containing the TFs
- atac_multiplex
The name of the multiplex containing the ATAC-seq peaks
- rna_multiplex
The name of the multiplex containing the RNA-seq genes
- multilayer_f
The folder where the multilayer is stored
- gene_list
A vector of genes to be considered for the target_genes (filtering is done on the genes before inferring the target_genes)
- tf_list
A vector of TFs to be considered for the final target_genes (filtering is done on the TFs after inferring the target_genes)
- save
A boolean indicating if the target_genes should be saved
- output_f
The name of the file where the target_genes should be saved (if save == TRUE)
- return_df
A boolean indicating if the target_genes should be returned as a dataframe
- suffix_bipartites
A suffix to add to the bipartites names (to indicate the exact file location)
- njobs
The number of jobs to be used to compute of the target_genes