Get a table of all the significant interactions across categories

Usage

get_sig_deggs(deggs_object, assayDataName = 1, sig_threshold = 0.05)

Arguments

deggs_object: an object of class deggs generated by get_diffNetworks
assayDataName: name of the assayData of interest. If an unnamed list of data was given to get_diffNetworks, assayDataName here will be the number corresponding to the position of the data in the assayDataList provided before (i.e. if transcriptomic data was second in the list, a list of all its differential interactions can be obtained with assayDataName = 2, if only one data table was provided assayDataName must be 1). Default 1.
sig_threshold: threshold for significance. Default 0.05.

Value

a data.frame listing all the significant differential interactions found across categories for that particular omic data. This list can also be used to substitute or integrate feature selection in machine learning models for the prediction of the categories (see vignette).

Examples

data("synthetic_metadata")
data("synthetic_rnaseqData")
deggs_object <- get_diffNetworks(assayData = synthetic_rnaseqData,
                                 metadata = synthetic_metadata,
                                 category_variable = "response",
                                 verbose = FALSE,
                                 show_progressBar = FALSE,
                                 cores = 2)
get_sig_deggs(deggs_object, sig_threshold = 0.05) 
#>                              from       to      p.value        p.adj
#> Non_responder.TNF-TNFRSF1A    TNF TNFRSF1A 3.325023e-04 1.330009e-03
#> Non_responder.IL1B-IL1R2     IL1B    IL1R2 5.389195e-04 2.155678e-03
#> Non_responder.TGFB3-TGFBR1  TGFB3   TGFBR1 5.329071e-15 2.131628e-14
#> Non_responder.AKT2-MTOR      AKT2     MTOR 4.347083e-04 1.738833e-03
#> Responder.FANCD2-FAN1      FANCD2     FAN1 0.000000e+00 0.000000e+00
#> Responder.FASLG-FAS         FASLG      FAS 6.947839e-07 2.084352e-06
#> Responder.MAP2K2-MAPK3     MAP2K2    MAPK3 1.153300e-12 3.459899e-12