| bigmelon-package | Write large-scale Illumina array datasets to CoreArray Genomic Data Structure (GDS) data files for efficient storage, access, and modification. |
| '[.gds.class' | Bigmelon accessors |
| '[.gdsn.class' | Bigmelon accessors |
| .getEstimate2 | Bumphunter using bigmelon |
| .sortvector | Compute the quantiles and ranks for a given gdsn.node |
| app2gds | Append a MethyLumiSet object to a preexisting gds file |
| backup.gdsn | Copy gds node to a backup folder within gds object |
| betaqn-method | Bigmelon Quantile Normalization methods. |
| betas-method | Bigmelon accessors |
| bigmelon | Write large-scale Illumina array datasets to CoreArray Genomic Data Structure (GDS) data files for efficient storage, access, and modification. |
| bigmelon-accessors | Bigmelon accessors |
| bigPepo | tea.gds - description and validation for gds objects |
| bumphunterEngine.gdsn | Bumphunter using bigmelon |
| cantaloupe | Small MethyLumi 450k data sets for testing |
| chainsaw | Chainsaw - modify gds file by subsetting all nodes |
| colnames-method | Bigmelon accessors |
| combo.gds | Combine two different gds objects together |
| computebeta.gds | Dasen Quantile Normalization by storing ranks |
| danen-method | Bigmelon Quantile Normalization methods. |
| danen.gds | Bigmelon Quantile Normalization methods. |
| danes-method | Bigmelon Quantile Normalization methods. |
| danes.gds | Bigmelon Quantile Normalization methods. |
| danet-method | Bigmelon Quantile Normalization methods. |
| danet.gds | Bigmelon Quantile Normalization methods. |
| dasen-method | Bigmelon Quantile Normalization methods. |
| dasen.gds | Bigmelon Quantile Normalization methods. |
| dasenrank | Dasen Quantile Normalization by storing ranks |
| daten1-method | Bigmelon Quantile Normalization methods. |
| daten1.gds | Bigmelon Quantile Normalization methods. |
| daten2-method | Bigmelon Quantile Normalization methods. |
| daten2.gds | Bigmelon Quantile Normalization methods. |
| db.gdsn | Bigmelon Quantile Normalization methods. |
| dfsfit.gdsn | Bigmelon Quantile Normalization methods. |
| dim.gds.class | dim.gds.class S3 method returning dimensions of data represented by a gds file handle. |
| dmrse-method | Functions imported from wateRmelon |
| dmrse_col-method | Functions imported from wateRmelon |
| dmrse_row-method | Functions imported from wateRmelon |
| es2gds | Coersion method for MethyLumiSet, RGChannelSet or MethylSet to CoreArray Genomic Data Structure (GDS) data file |
| estimateCellCounts.gds | Cell Proportion Estimation using bigmelon |
| exprs-method | Bigmelon accessors |
| fData-method | Bigmelon accessors |
| finalreport2gds | Read finalreport files and convert to genomic data structure files |
| fot | Bigmelon accessors |
| fot-method | Bigmelon accessors |
| gds2mlumi | Convert Genomic Data Structure file to Methylumiset or Methylset object. |
| gds2mset | Convert Genomic Data Structure file to Methylumiset or Methylset object. |
| genki-method | Functions imported from wateRmelon |
| geotogds | Download data from GEO and convert it into a gdsfmt object |
| getHistory-method | Bigmelon accessors |
| getpheno | Download data from GEO and convert it into a gdsfmt object |
| getquantiles | Cell Proportion Estimation using bigmelon |
| getquantilesandranks | Compute the quantiles and ranks for a given gdsn.node |
| honeydew | Small MethyLumi 450k data sets for testing |
| iadd | Add data from Illumina IDAT files to a gds file. |
| iadd2 | Add data from Illumina IDAT files to a gds file. |
| idats2gds | Add data from Illumina IDAT files to a gds file. |
| methylated-method | Bigmelon accessors |
| nanes-method | Bigmelon Quantile Normalization methods. |
| nanes.gds | Bigmelon Quantile Normalization methods. |
| nanet-method | Bigmelon Quantile Normalization methods. |
| nanet.gds | Bigmelon Quantile Normalization methods. |
| nasen-method | Bigmelon Quantile Normalization methods. |
| nasen.gds | Bigmelon Quantile Normalization methods. |
| naten-method | Bigmelon Quantile Normalization methods. |
| naten.gds | Bigmelon Quantile Normalization methods. |
| pData-method | Bigmelon accessors |
| pfilter,gds.class | Basic data filtering for Illumina methylation data in gds objects |
| pfilter-method | Basic data filtering for Illumina methylation data in gds objects |
| pfilter.gds | Basic data filtering for Illumina methylation data in gds objects |
| prcomp, gds.class | Principal Component Analysis for high-dimensional data |
| prcomp-method | Principal Component Analysis for high-dimensional data |
| prcomp.gds | Principal Component Analysis for high-dimensional data |
| prcomp.gds.class | Principal Component Analysis for high-dimensional data |
| predictSex | Functions imported from wateRmelon |
| predictSex-method | Functions imported from wateRmelon |
| pvals-method | Bigmelon accessors |
| pwod, gds.class | Probe-Wise Outlier Detection for DNA methylation data. |
| pwod, gdsn.class | Probe-Wise Outlier Detection for DNA methylation data. |
| pwod.gdsn | Probe-Wise Outlier Detection for DNA methylation data. |
| QCmethylated | Bigmelon accessors |
| QCmethylated-method | Bigmelon accessors |
| QCrownames | Bigmelon accessors |
| QCrownames-method | Bigmelon accessors |
| QCunmethylated | Bigmelon accessors |
| QCunmethylated-method | Bigmelon accessors |
| qn.gdsn | Bigmelon Quantile Normalization methods. |
| qual-method | Functions imported from wateRmelon |
| redirect.gds | Change the location of the paths for row and column names in a gds file. |
| rownames-method | Bigmelon accessors |
| seabi-method | Functions imported from wateRmelon |
| unmethylated-method | Bigmelon accessors |
| wm-port | Functions imported from wateRmelon |