OmicsPathway-class.RdAn S4 class for mass spectrometry or bio-assay data and gene pathway lists
assayData_dfAn \(N \times p\) data frame with named columns.
sampleIDs_charA character vector with the N sample names.
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.
trimPathwayCollectionA subset of the list stored in the
pathwayCollection slot. This list will have pathways that only
contain genes that are present in the assay data frame.