marina-methods: Inference of Master Regulators

In diggit: Inference of Genetic Variants Driving Cellular Phenotypes

Description

This function infers the master regulators for the transition between two phenotypes

Usage

marina(x, ...)

## S4 method for signature 'matrix'
marina(x, y = NULL, mu = 0, regulon, per = 1000,
  cores = 1, verbose = TRUE)

## S4 method for signature 'ExpressionSet'
marina(x, pheno = "cond", group1, group2 = NULL,
  mu = 0, regulon, per = 1000, cores = 1, verbose = TRUE)

## S4 method for signature 'diggit'
marina(x, pheno, group1, group2 = NULL, mu = 0,
  regulon = NULL, per = 1000, cores = 1, verbose = TRUE)

Arguments

x	Object of class diggit, expressionSet object or numerical matrix containing the test samples
...	Additional arguments
y	Numerical matrix containing the control samples
mu	Number indicating the control mean when y is ommited
regulon	Transcriptional interactome
per	Interger indicating the number of permutations to compute the marina null model
cores	Integer indicating the number of cores to use (1 for Windows-based systems)
verbose	Logical, whether progress should be reported
pheno	Character string indicating the phenotype data to use
group1	Vector of character strings indicating the category from phenotype pheno to use as test group
group2	Vector of character strings indicating the category from phenotype pheno to use as control group

Value

Updated diggit object with Master Regulator results

Examples

cores <- 3*(Sys.info()[1] != "Windows")+1
data(gbm.expression, package="diggitdata")
data(gbm.aracne, package="diggitdata")

eset <- exprs(gbmExprs)
samples <- pData(gbmExprs)[["subtype"]]
x <- eset[, samples=="MES"]
y <- eset[, samples=="PN"]
dgo <- marina(x, y, regulon=gbmTFregulon, per=100, cores=cores)
dgo
diggitMR(dgo)[1:5]
dgo <- marina(gbmExprs, pheno="subtype", group1="MES", group2="PN", regulon=gbmTFregulon, per=100, cores=cores)
dgo
diggitMR(dgo)[1:5]
x <- diggitClass(expset=gbmExprs, regulon=gbmTFregulon)
dgo <- marina(x, pheno="subtype", group1="MES", group2="PN", per=100, cores=cores)
dgo
diggitMR(dgo)[1:5]

diggit documentation built on Nov. 8, 2020, 8:18 p.m.