Get a table of all significant interactions across categories

Usage

get_multiOmics_diffNetworks(deggs_object, sig_threshold = 0.05)

Arguments

deggs_object: an object of class deggs generated by get_diffNetworks
sig_threshold: threshold for significance. Default 0.05.

Value

a list of multilayer networks (as edge tables), one per category.

Examples

data("synthetic_metadata")
data("synthetic_rnaseqData")
data("synthetic_proteomicData")
data("synthetic_OlinkData")
assayData_list <- list("RNAseq" = synthetic_rnaseqData,
                       "Proteomics" = synthetic_proteomicData,
                       "Olink" = synthetic_OlinkData)
deggs_object <- get_diffNetworks(assayData = assayData_list,
                                 metadata = synthetic_metadata,
                                 category_variable = "response",
                                 verbose = FALSE,
                                 show_progressBar = FALSE,
                                 cores = 2)
get_multiOmics_diffNetworks(deggs_object, sig_threshold = 0.05)
#> $Non_responder
#>                  from       to      p.value        p.adj      layer
#> TNF-TNFRSF1A      TNF TNFRSF1A 3.325023e-04 1.330009e-03     RNAseq
#> IL1B-IL1R2       IL1B    IL1R2 5.389195e-04 2.155678e-03     RNAseq
#> TGFB3-TGFBR1    TGFB3   TGFBR1 5.329071e-15 2.131628e-14     RNAseq
#> AKT2-MTOR        AKT2     MTOR 4.347083e-04 1.738833e-03     RNAseq
#> FANCD2-FAN1    FANCD2     FAN1 4.440892e-16 3.552714e-15 Proteomics
#> GNG12-RASA2     GNG12    RASA2 0.000000e+00 0.000000e+00 Proteomics
#> RASGRP3-RRAS  RASGRP3     RRAS 2.202344e-04 1.761875e-03 Proteomics
#> TNF-TNFRSF1A1     TNF TNFRSF1A 0.000000e+00 0.000000e+00 Proteomics
#> RASGRP1-RAP1A RASGRP1    RAP1A 2.840564e-03 2.272452e-02 Proteomics
#> 
#> $Responder
#>                from    to      p.value        p.adj  layer
#> FANCD2-FAN1  FANCD2  FAN1 0.000000e+00 0.000000e+00 RNAseq
#> FASLG-FAS     FASLG   FAS 6.947839e-07 2.084352e-06 RNAseq
#> MAP2K2-MAPK3 MAP2K2 MAPK3 1.153300e-12 3.459899e-12 RNAseq
#>