README.md

In xinchoubiology/Rcppsva: Rcpp Integration Surrogate Variable Analysis

Package Rcppsva : Package of comprehensive differential methylation region motif search engine

package reconstruction path: generic definition : AllGeneric.R class definition : AllClasses.R * Flowchart: + Raw data reading : minfi package - minfi::preprocessRaw - minfi::preprocessIllumina - minfi::getBeta minfi::getM - minfi::preprocessSWAN

• Batch effect elimination : combat.R

  • ComBat

• Surrogate variable analysis : sva.R

  • estDimRMT
  • isva

• Normalized beta/M value expression matrix ~ design matrix(phenotype + surrogate variables) : sva.R

  • svaReg

• Sampling null distribution for coefficient of phenotype : sampling.R

  • mlm.fit : permutation sampling
  • bootstrap.fit : bootstrap sampling

• Clustering CpG sites by distance : misc.R( Given spatial constraint on genome )

  • agglomerateBydist
  • diffbumpFilter (filter Bumps by difference p-value of null distribution)
  • corrbumpFilter (filter Bumps by correlation constraint of null distribution)

• Dbpmerge -- Agglomerative clustering for correlation CpG regions search : merge.R

  • Dbpmerge (Pre-clustered region are tested by combinePval method)

• Combin p-value method via stouffer-liptik method : combp.R

  • combinep (combine pvalue method)
  • stoufferliptakCombp
  • zscoreCombp

• Local weight smooth method : lowess.R

  • lowess

• Hierachical clustering : hclust.R

  • eigenM : representing M of DMR(regions) by eigen-value & sample-wise mean
  • hclust
  • referenceDist
  • gapStat
  • optimalHC
  • ultilities: util.R:
  • dendrogram dispatch methods

• Auxiliary function : dendrogram.R

  • dendrogram plot [not necessary]

• Unirform interface : bumphunter.R

  • bumphunterEigen

• TCGA-Assembler Downloading : get450K.R

  • downloadMethylURL
  • getClinical
  • getMethyltion
  • get450K (read in methylation 450K data and coefficients)

• BMarry Class abstraction

  • methods wrapper for all above methods

• 450K preprocessing

  • getTCGAssemble (load TCGA Assembler Package in /inst)
  • get450Kurl
  • get450Ksheet
  • get450Kzip

xinchoubiology/Rcppsva documentation built on May 4, 2019, 1:06 p.m.