Display the Summary of an Omics*-class Object.

The display method for objects of class OmicsPathway, OmicsSurv, OmicsReg, or OmicsCateg.

# S4 method for OmicsPathway
show(object)

Arguments

object	An object inheriting the super-class OmicsPathway. This class includes objects of class OmicsSurv, OmicsReg, or OmicsCateg.

Value

A copy of object, returned invisibly (with the invisible function).

Details

S4 objects print to the screen via the show function. This function sets a show method for OmicsPathway objects.

Examples

  ###  Load the Example Data  ###
  data("colonSurv_df")
  data("colon_pathwayCollection")

  ###  Create an OmicsSurv Object  ###
  colon_OmicsSurv <- CreateOmics(
    assayData_df = colonSurv_df[, -(2:3)],
    pathwayCollection_ls = colon_pathwayCollection,
    response = colonSurv_df[, 1:3],
    respType = "surv"
  )
#> 
#>   ======  Creating object of class OmicsSurv  =======
#> The input pathway database included 676 unique features.
#> The input assay dataset included 656 features.
#> Only pathways with at least 3 or more features included in the assay dataset are
#>   tested (specified by minPathSize parameter). There are 15 pathways which meet
#>   this criterion.
#> Because pathwayPCA is a self-contained test (PMID: 17303618), only features in
#>   both assay data and pathway database are considered for analysis. There are 615
#>   such features shared by the input assay and pathway database.

  ###  Print / Show  ###
  colon_OmicsSurv
#> Formal class 'OmicsSurv' [package "pathwayPCA"] with 6 slots
#>   ..@ eventTime            : num [1:250] 64.9 59.8 62.4 54.5 46.3 ...
#>   ..@ eventObserved        : logi [1:250] FALSE FALSE FALSE FALSE TRUE FALSE ...
#>   ..@ assayData_df         :Classes 'tbl_df', 'tbl' and 'data.frame':	250 obs. of  656 variables:
#>   ..@ sampleIDs_char       : chr [1:250] "subj1" "subj2" "subj3" "subj4" ...
#>   ..@ pathwayCollection    :List of 3
#>   .. ..- attr(*, "class")= chr [1:2] "pathwayCollection" "list"
#>   ..@ trimPathwayCollection:List of 4
#>   .. ..- attr(*, "class")= chr [1:2] "pathwayCollection" "list"