generate_subnetworks: Generate subnetworks

In elisabettasciacca/DEGGs: Differentially Expressed Gene-Gene pairs

Generate subnetworks

Description

Generate subgroup specific gene-gene interaction networks with interaction p values

Usage

generate_subnetworks(
  normalised_counts,
  metadata,
  subgroup_variable,
  regression_method = "rlm",
  subgroups = NULL,
  network = NULL,
  entrezIDs = FALSE,
  convert_to_gene_symbols = TRUE,
  use_qvalues = FALSE,
  cores = parallel::detectCores()/2
)

Arguments

normalised_counts	a data frame containing normalised counts from an high throughput sequencing experiment. Sample IDs must be in columns and gene/miRNA/TFs in rows. Objects of class matrix are not allowed.
metadata	a data frame of sample data with rownames matching the sample IDs in normalised_counts colnames
subgroup_variable	column name in metadata that contains the subgroup identifier for each sample in normalised_counts
regression_method	whether to use robust linear modelling to calculate link p values. Options are 'rlm' (default) or 'lm'.
subgroups	optional character vector indicating which subgroups must be used for comparison. If not specified, all subgroups in subgroup_variable will be used.
network	network of biological interactions provided by the user. The network must be provided in the form of a table of class data.frame with two columns named "from" and "to". If NULL (default) a network of 10,537 molecular interactions obtained from KEGG, mirTARbase, miRecords and transmiR will be used. This has been obtained via the exportgraph function of the MITHrIL tool (Alaimo et al., 2016).
entrezIDs	logical (default FALSE) used to define whether gene ids in normalised_counts are entrez ids (TRUE) or gene symbols (FALSE).
convert_to_gene_symbols	logical to be used when using entrez ids. If TRUE (default), the output will show gene symbols.
use_qvalues	whether to use Storey's q values for multiple test adjustment. If FALSE (default), unadjusted p values will be used and shown in the output.
cores	number of cores to use.

Value

a deggs object containing subgroup specific networks incorporating p values or adjusted p values for each link.

See Also

deggs.

elisabettasciacca/DEGGs documentation built on April 27, 2024, 12:51 a.m.