Man pages for jgygi/SPEAR
SPEAR - Sparse Supervised Bayesian Factor Model for Multi-omic Analyses
| add.data | Add a dataset to a SPEAR object. |
| assess | Assess the predictions from the SPEAR model using a variety... |
| check.fit | Check if a fit object is generated and if a weight has been... |
| check.fold.ids | Confirm fold.ids will work in cv.spear |
| create.params | Create the parameters for SPEAR. Private method. |
| cv.evaluate | Evaluate cv SPEAR object |
| encode.ordinal | Encode a matrix or data.frame (Y) into ordinal (0, 1, 2, ...) |
| estimate.num.factors | Estimate the number of factors needed for the SPEAR model. |
| generate.fold.ids | Randomly generate fold.ids to be used for reproducibility in... |
| generate.spear.ids | Randomly generate identifiers for analytes (to prevent... |
| get.analyte.scores | Get features from a SPEAR object. |
| get.concatenated.X | Randomly generate identifiers for analytes (to prevent... |
| get.cv.loss | Get the loss from the cross validation. Must be called from a... |
| get.data | Extract a dataset from a SPEAR object. |
| get.factor.contributions | Get factor contributions to response prediction from a SPEAR... |
| get.factor.scores | Get factor scores from a SPEAR object for a particular... |
| get.predictions | Get predictions from a SPEARobject and a dataset 'data'. |
| get.signatures | Get features from a SPEARobject. |
| get.variance.explained | Get variance explained per assay from a SPEAR object. |
| get.widx.from.method | Get a w.idx from a method (private function, can't be called... |
| get.Y | Randomly generate identifiers for analytes (to prevent... |
| new.spear | Make a SPEARobject. Will return an R6 class SPEARobject used... |
| one.hot.encode.multinomial | One-hot encode a matrix or data.frame (Y) |
| plot.cv.loss | Get the loss from the cross validation. Must be called from a... |
| plot.factor.contributions | Plot variance explained for a SPEAR object. |
| plot.factor.scores | Plot factor scores from a SPEARobject for a particular... |
| plot.variance.explained | Plot variance explained for a SPEAR object. |
| print.out | Print out a variety of summary information about a... |
| remove.data | Remove a dataset from a SPEAR object. |
| set.color.scheme | Set the colors for a SPEAR object, to be used in plotting... |
| set.response | Choose a response to be preferred for plotting functions.... |
| set.weights | Choose a combination of weights for a SPEAR object. Print... |
| spear | SPEAR - SuPervised Bayes fActor for Multi-omics imports: |
| train.spear | Run SPEAR |
| update.dimnames | Update the dimension names for all SPEARobject matrices. Used... |
