interactionGeneTable: Generate table with genes classified into a mathematically...

In taylo5jm/interactions: Classification of gene expression profile sets generated from combination stimuli

Description

Generate table with genes classified into a mathematically defined interaction mode

Usage

interactionGeneTable(v, modes, log.fcs, pw_s, classes,
  exclude.null.vector = TRUE, exclusivity.vectors = FALSE,
  DRUG_COMBINATION = TRUE, ...)

Arguments

v	EList constructed with voom
modes	Character vector of length n indicating interaction modes of genes
log.fcs	Numeric matrix of log fold changes generated from the limma or edgeR pipelines
classes	Character vector of interaction classes for n genes. If missing, getIntClass() is called to assign interaction classes to each interaction mode.
exclude.null.vector	Boolean TRUE when genes with the null outcome vector (0, 0, 0, 0, 0, 0) should be excluded from the table.
exclusivity.vectors	Boolean FALSE when exclusivity vectors should be excluded from the table.

Value

data.frame with outcome vectors, interaction classes & modes, fold changes for all genes classified into an interaction class

taylo5jm/interactions documentation built on May 31, 2019, 3:57 a.m.