Deggs-class: An S4 class to define the deggs output

In elisabettasciacca/DEGGs: Differentially Expressed Gene-Gene pairs

An S4 class to define the deggs output

Description

An S4 class to define the deggs output

Slots

subnetworks

a list of data frames containing the subgroup networks and a number indicating the total count of links that reached significance in all subgroups (considering p or adj p < 0.05)

normalised_counts

a data frame containig the normalised count data given in input.

metadata

a data frame of sample data given in input and matching the sample IDs in normalised_counts.

subgroup_variable

column name in metadata that contains the subgroup definition for each sample in normalised_counts.

regression_method

the chosen regression method used to calculate interaction p values. It can be either 'rlm' or 'lm'.

subgroups

character vector indicating which subgroups are used for comparison.

use_qvalues

logical. Indicates whether p values are adjusted via Storey's q value method

elisabettasciacca/DEGGs documentation built on April 17, 2025, 5:41 a.m.