fetch.mee |
fetch.mee to generate MEE.data class object. |
fetch.pair |
fetch.pair to generate Pair class object. |
get.diff.meth |
get.diff.meth to identify hypo/hyper-methylated CpG sites on HM450K between control and experimental groups such as normal verus tumor samples. |
get.enriched.motif |
get.enriched.motif to identify the overrepresented motifs in a set of probes (HM450K) regions. |
get.feature.probe |
get.feature.probe to select probes within promoter regions or distal regions. |
get.pair |
get.pair to predict enhancer-gene linkages. |
get.permu |
get.permu to generate permutation results for calculation of empirical P values for each enhancer-gene linkage. |
get.TFs |
get.TFs to identify regulatory TFs. |
get450K |
get450K to download HM40K DNA methylation data for certain cancer types from TCGA website. |
getClinic |
getClinic to download clinic data for certain cancer types from TCGA website. |
getExp |
getExp to extract RNA expression slot from a MEE.data class object. |
getExp-method |
getExp to extract RNA expression slot from a MEE.data class object. |
getGeneID |
getGeneID to report gene id from symbol |
getGeneInfo |
getGeneInfo to extract geneInfo slot from MEE.data or Pair object. |
getGeneInfo-method |
getGeneInfo to extract geneInfo slot from MEE.data or Pair object. |
getMeth |
getMeth to extract DNA methylation slot from a MEE.data class object. |
getMeth-method |
getMeth to extract DNA methylation slot from a MEE.data class object. |
GetNearGenes |
GetNearGenes to collect nearby genes for one locus. |
getPair |
getPair to extract pairInfo slot from Pair object. |
getPair-method |
getPair to extract pairInfo slot from Pair object. |
getProbeInfo |
getProbeInfo to extract probeInfo slot from MEE.data or Pair object. |
getProbeInfo-method |
getProbeInfo to extract probeInfo slot from MEE.data or Pair object. |
getRNAseq |
getRNAseq to download all RNAseq data for a certain cancer type from TCGA. |
getSample |
getSample to extract sample information from MEE.data object. |
getSample-method |
getSample to extract sample information from MEE.data object. |
getSymbol |
getSymbol to report gene symbol from id |
getTCGA |
getTCGA to download DNA methylation, RNA expression and clinic data for all samples of certain cancer type from TCGA. |
MEE.data-class |
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. |
motif.enrichment.plot |
motif.enrichment.plot to plot bar plots showing motif enrichment ORs and 95% confidence interval for ORs |
Pair-class |
An S4 class that pairs information, probe information and gene information. |
promoterMeth |
promoterMeth to calculate associations of gene expression with DNA methylation at promoter regions. |
scatter.plot |
scatter.plot to plot scatter plots between gene expression and DNA methylation. |
schematic.plot |
schematic.plot to plot schematic plots showing the locations of genes and probes. |
TCGA.pipe |
ELMER analysis pipeline for TCGA data. |
TF.rank.plot |
TF.rank.plot to plot the scores (-log10(P value)) which assess the correlation between TF expression and average DNA methylation at motif sites. |
txs |
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. |