View source: R/use_ligand_to_target.R
get_target_genes_ligand_oi | R Documentation |
get_target_genes_ligand_oi
Get a set of predicted target genes of a ligand of interest.
get_target_genes_ligand_oi(ligand_oi, ligand_target_matrix, error_rate = 0.1, cutoff_method = "distribution", fdr_method = "global", output = "logical",ligands_position = "cols")
ligand_oi |
The ligand of interest of which top target genes should be returned |
ligand_target_matrix |
A matrix of ligand-target probabilty scores. |
error_rate |
FDR for cutoff_method "fdrtool" and "distribution"; number between 0 and 1 indicating which top fraction of target genes should be returned for cutoff_method "quantile". Default: 0.1 |
cutoff_method |
Method to determine which genes can be considered as a target of a ligand and which genes not, based on the ligand-target probability scores. Possible options: "distribution", "fdrtool" and "quantile". Default: "distribution". |
fdr_method |
Only relevant when cutoff_method is "fdrtool". Possible options: "global" and "local". Default: "global". |
output |
Determines whether a vector with target gene names should be returned ("gene_symbols") or a logical vector indicating for every target gene whether or not it is a target ("logical"). |
ligands_position |
Indicate whether the ligands in the ligand-target matrix are in the rows ("rows") or columns ("cols"). Default: "cols" |
A vector with target gene names should be returned ("gene_symbols") or a logical vector indicating for every target gene whether or not it is a target ("logical").
## Not run:
## Generate the ligand-target matrix from loaded weighted_networks
weighted_networks = construct_weighted_networks(lr_network, sig_network, gr_network,source_weights_df)
ligands = list("TNF","BMP2",c("IL4","IL13"))
ligand_target_matrix = construct_ligand_target_matrix(weighted_networks, ligands)
targets = get_target_genes_ligand_oi("BMP2", ligand_target_matrix, error_rate = 0.1, cutoff_method = "distribution", fdr_method = "global", output = "logical",ligands_position = "cols")
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.