Man pages for JoshuaTian/ChAMP
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
| Block.GUI | Generate interactive plot for the result of champ.Block()... |
| champ.Block | Identify Differential Methylation Blocks in Illumina... |
| champ.CNA | Inference of Copy Number Abberrations from intensity values. |
| champ.DMP | Identify Differential Methylation Positions (DMP) and Numeric... |
| champ.DMR | Applying Bumphunter, DMRcate or ProbeLasso Algorithms to... |
| champ.ebGSEA | Empirical Bayes GSEA method. |
| champ.filter | Do filtering on beta, M, intensity, Meth and UnMeth matrix. |
| champ.GSEA | Do GSEA for DMP, DMR and other methylation data related... |
| champ.import | Read data from IDAT file. |
| champ.impute | Conduct imputation for NA value on beta matrix and... |
| champ.load | Upload of raw HumanMethylation450K or HumanMethylationEPIC... |
| champ.norm | Normalization for HumanMethylation450 or HumanMethylationEPIC... |
| ChAMP-package | ChAMP-Chip Analysis Methylation Pipeline |
| champ.process | Process function to run all methods in ChAMP pipeline. |
| champ.QC | Plot quality control plot, mdsplot, densityPlot, dendrogram... |
| champ.refbase | Applying References-Base Methold to beta valued methylation... |
| champ.runCombat | Function that uses ComBat to correct for batch effects.... |
| champ.SVD | Singular Value Decomposition analysis for batch effects... |
| CpG.GUI | Generate interactive plot for summary information of a list... |
| DMP.GUI | Generate interactive plot for the result of champ.DMP()... |
| DMR.GUI | Generate interactive plot for the result of champ.DMR()... |
| QC.GUI | Generate interactive plot for Quality Control of a dataset |
