calc_pvalues_network: Calculate the pvalues for specific subgroup network samples

In elisabettasciacca/DEGGs: Differentially Expressed Gene-Gene pairs

Calculate the pvalues for specific subgroup network samples

Description

Calculate the pvalues for specific subgroup network samples

Usage

calc_pvalues_network(
  normalised_counts,
  metadata,
  sig_var,
  subgroup_variable,
  subgroups_length,
  regression_method = "rlm",
  subgroup_network
)

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
sig_var	Inherited from generate_subnetworks. It can be q.value or p.value depending on how use_qvalues was set in the generate_subnetworks function (default FALSE).
subgroup_variable	column name in metadata that contains the subgroup identifier for each sample in normalised_counts
subgroups_length	integer number indicating the number of subgroups
regression_method	whether to use robust linear modelling to obtain p value of the interactions. Options are 'rlm' (default) or 'lm'
subgroup_network	network table for a specific subgroup

Value

a list of p values

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