TCGA.pipe: ELMER analysis pipeline for TCGA data.

In lijingya/ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

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)

lijingya/ELMER documentation built on May 21, 2019, 6:14 a.m.