deggs-class | R Documentation |

An S4 class to define the deggs output

`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

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