Genome-Wide DNA Methylation Sites Screening by Use of Training and Testing Samples
ttScreening with Firth bias-reduced logistic regression + multiple tes...
Adjusted irwsva.build which builds surrogate variables from gene expre...
Adjusted num.sv which estimates the number of important surrogate vari...
Rare_Screening: resampling-based screening with limma
The adjusted sva code using irwsva.build2
Genome-Wide DNA Methylation Sites Screening by Use of Training and Tes...
A screening process built upon training and testing samples
A screening process utilizing training and testing samples to filter out uninformative DNA methylation sites. Surrogate variables (SVs) of DNA methylation are included in the filtering process to explain unknown factor effects. This package also provides two screening functions for screening high-dimensional predictors when the events are rare. The firth method is called 'Rare-Screening' which employs a repeated random sampling with replacement and using linear modeling with Bayes adjustment. The Second method is called 'Firth-ttScreening' which uses 'ttScreening' method with additional Firth correction term in the maximum likelihood for the logistic regression model. These methods handle the high-dimensionality and low event rates.