BioM2 Hyperparametric Combination
HyBioM2(
TrainData = NULL,
pathlistDB = NULL,
FeatureAnno = NULL,
resampling = NULL,
nfolds = 5,
classifier = "liblinear",
predMode = "probability",
PathwaySizeUp = 200,
PathwaySizeDown = 20,
MinfeatureNum_pathways = 10,
Add_UnMapped = TRUE,
Add_FeartureSelection_Method = "wilcox.test",
Unmapped_num = 300,
Inner_CV = TRUE,
inner_folds = 10,
Stage1_FeartureSelection_Method = "cor",
stage1_cutoff = 0.3,
Stage2_FeartureSelection_Method = "RemoveHighcor",
stage2_cutoff = 0.8,
classifier2 = NULL,
cores = 1,
verbose = TRUE
)A data frame contains hyperparameter results
The input training dataset. The first column is the label or the output. For binary classes, 0 and 1 are used to indicate the class member.
A list of pathways with pathway IDs and their corresponding genes ('entrezID' is used). For details, please refer to ( data("GO2ALLEGS_BP") )
The annotation data stored in a data.frame for probe mapping. It must have at least two columns named 'ID' and 'entrezID'. (For details, please refer to data( data("MethylAnno") )
Resampling in mlr3verse.
k-fold cross validation ( Only supported when TestData = NULL )
Learners in mlr3
The prediction mode. Currently only supports 'probability' for binary classification tasks.
The upper-bound of the number of genes in each biological pathways.
The lower-bound of the number of genes in each biological pathways.
The minimal defined pathway size after mapping your own data to pathlistDB(KEGG database/GO database).
Whether to add unmapped probes for prediction
Feature selection methods.
The number of unmapped probes
Whether to perform a k-fold verification on the training set.
k-fold verification on the training set.
Feature selection methods.
The cutoff used for feature selection threshold. It can be any value between 0 and 1.
Feature selection methods.
The cutoff used for feature selection threshold. It can be any value between 0 and 1.
Learner for stage 2 prediction(if classifier2==NULL,then it is the same as the learner in stage 1.)
The number of cores used for computation.
Whether to print running process information to the console