OmicsSurv-class: An S4 class for survival responses within an 'OmicsPathway'...

In pathwayPCA: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Description

This creates the OmicsSurv class which extends the OmicsPathway master class.

Slots

assayData_df

An N \times p data frame with named columns.

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.

eventTime

A numeric vector with N observations corresponding to the last observed time of follow up.

eventObserved

A logical vector with N observations indicating right-censoring. The values will be FALSE if the observation was censored (i.e., we did not observe an event).

See Also

OmicsPathway, CreateOmics

pathwayPCA documentation built on Dec. 15, 2020, 6:14 p.m.