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

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