HOmics.meth: Integrates methylation and gene data

In lnonell/HOmics: Hierarchical omics

Description

Integrates methylation and gene data

Usage

HOmics.meth(meth.data = GRSet, pheno.cond.col = "tissue.ch1",
  annot.gene.col = "UCSC_RefGene_Name",
  annot.z.col = c("UCSC_RefGene_Group"), annot.mult.sep = ";",
  z.matrix = NULL, pheno.covar.col = NULL, gene.list = genes.u,
  seed = NULL, cores = 1, n.adapt = 1000, n.chains = 3,
  n.iter = 2000, ...)

Arguments

meth.data	GenomicRatioSet or ExpressionSet with methylation data
pheno.cond.col	response variable, column of annotation that contains condition (one of the variable names contained in pheno data obtained with function pData())
annot.gene.col	column of annotation that contains gene names (same annotations as gene.list). Default = "UCSC_RefGene_Name"
annot.z.col	prior information. Column of annotation that contains prior variable (for GenomicRatioSet functions getAnnotation() or fData() for ExpressionSet). Default = "UCSC_RefGene_Group"
annot.mult.sep	separator for annot.gene.col and maybe annot.z.col multiple values. Default = ";"
z.matrix	prior information. Alternative parameter to annot.z.col as matrix with rows the featureNames of meth.data and columns the Zvars can be given. Default = NULL
pheno.covar.col	covariates, column of annotation that contains names of covariates to include in the model (one or more of the variable names contained in pheno data). Default = NULL
gene.list	genes to analyze as a vector with symbols (HUGO)
seed	numerical seed for the use of function set.seed in the generation of the model, for reproducibility
cores	cores in case of parallelization. Default = 1 (no parallelization)
n.adapt	number of iterations for the adaptative phase of the hierarchical model. Default = 1000
n.iter	number of iteractions for the burn in phase or sampling of the hierarchical model. Default = 2000
n.chain	number of chains of the hierarchical model. Default = 3

Value

an object of class HOmics

Examples

to be built

lnonell/HOmics documentation built on July 23, 2019, 1:10 a.m.