ELMER (version 1.4.2)

TCGA.pipe: ELMER analysis pipeline for TCGA data.

Description

ELMER analysis pipeline for TCGA data. This pipeline combine every steps of ELMER analyses: get.feature.probe, get.diff.meth, get.pair, get.permu, get.enriched.motif and get.TFs. Every steps' results are saved.

Usage

TCGA.pipe(disease, analysis = "all", wd = "./", cores = NULL, Data = NULL, diff.dir = "hypo", ...)

Arguments

disease

TCGA disease name in short form such as COAD

analysis

A vector of characters listing the analysis need to be done. Analysis can be "download","distal.probes","diffMeth","pair","motif","TF.search". Default is "all" meaning all the analysis will be processed.

wd

A path shows working dirctory. Default is "./"

cores

A interger defines number of core to be used in parallel process. Default is NULL: don't use parallel process.

Data

A path shows the folder containing DNA methylation, expression and clinic data

diff.dir

A character can be "hypo" or "hyper", showing dirction DNA methylation changes. If it is "hypo", get.diff.meth function will identify all significantly hypomethylated CpG sites; If "hyper", get.diff.meth function will identify all significantly hypermethylated CpG sites

...

A list of parameters for functions: GetNearGenes, get.feature.probe, get.diff.meth, get.pair,

Value

Different analysis results.

Examples

## Not run: 
# distal.probe <- TCGA.pipe(disease = "LUSC", analysis="Probe.selection", wd="~/")
# ## End(Not run)