OmicsPathway-class.Rd
An S4 class for mass spectrometry or bio-assay data and gene pathway lists
assayData_df
An \(N \times p\) data frame with named columns.
sampleIDs_char
A character vector with the N sample names.
pathwayCollection
A 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.
trimPathwayCollection
A 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.