OmicsPathway objectOmicsCateg-class.RdThis creates the OmicsCateg class which extends the
OmicsPathway master class.
assayData_dfAn \(N \times p\) data frame with named columns.
pathwayCollectionA list of known gene pathways with three or four elements:
pathways : A named list of character vectors. Each vector
contains the names of the individual genes within that pathway as a
vector of character strings. The names contained in these vectors must
have non-empty overlap with the column names of the
assayData_df data frame. The names of the pathways (the list
elements themselves) should be the a shorthand representation of the
full pathway name.
TERMS : A character vector the same length as the
pathways list with the proper names of the pathways.
description : An optional character vector the same length
as the pathways list with additional information about the
pathways.
setsize : A named integer vector the same length as the
pathways list with the number of genes in each pathway. This list
item is calculated during the creation step of a CreateOmics
function call.
responseA factor vector of length \(N\): the dependent
variable of a generalized linear regression exercise. Currently, we
support binary factors only. We expect to extend support to n-ary
responses in the next package version.