Learn R Programming

ELMER (version 1.4.2)

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

Copy Link

Version

Version

1.4.2

License

GPL-3

Maintainer

Lijing Yao

Last Published

February 15th, 2017

Functions in ELMER (1.4.2)

MEE.data An S4 class contains 5 slots: methylation, expression, sample information, probe information and gene information. MEE.data class are the main input for main functions.

fetch.mee to generate MEE.data class object.

get.permu to generate permutation results for calculation of empirical P values for each enhancer-gene linkage.

get.feature.probe

get.feature.probe to select probes within promoter regions or distal regions.

getMeth to extract DNA methylation slot from a MEE.data class object.

getPair to extract pairInfo slot from Pair object.

get.diff.meth to identify hypo/hyper-methylated CpG sites on HM450K between control and experimental groups such as normal verus tumor samples.

getSymbol to report gene symbol from id

getRNAseq to download all RNAseq data for a certain cancer type from TCGA.

promoterMeth to calculate associations of gene expression with DNA methylation at promoter regions.

schematic.plot to plot schematic plots showing the locations of genes and probes.

GetNearGenes to collect nearby genes for one locus.

getGeneID to report gene id from symbol

getTCGA to download DNA methylation, RNA expression and clinic data for all samples of certain cancer type from TCGA.

txs to fetch USCS gene annotation (transcripts level) from Bioconductor package Homo.sapians. If upstream and downstream are specified in TSS list, promoter regions of USCS gene will be generated.

getClinic to download clinic data for certain cancer types from TCGA website.

getProbeInfo to extract probeInfo slot from MEE.data or Pair object.

get.enriched.motif

get.enriched.motif to identify the overrepresented motifs in a set of probes (HM450K) regions.

get.TFs to identify regulatory TFs.

TF.rank.plot to plot the scores (-log10(P value)) which assess the correlation between TF expression and average DNA methylation at motif sites.

motif.enrichment.plot

motif.enrichment.plot to plot bar plots showing motif enrichment ORs and 95% confidence interval for ORs

An S4 class that pairs information, probe information and gene information.

getGeneInfo to extract geneInfo slot from MEE.data or Pair object.

fetch.pair to generate Pair class object.

get.pair to predict enhancer-gene linkages.

getExp to extract RNA expression slot from a MEE.data class object.

scatter.plot to plot scatter plots between gene expression and DNA methylation.

ELMER analysis pipeline for TCGA data.

get450K to download HM40K DNA methylation data for certain cancer types from TCGA website.

getSample to extract sample information from MEE.data object.