Man pages for ahmedelmahy/RNASeqclassifier1
A collection of functions for feature selection and classifier development from RNASeq data.
| class_predict | Create confusion matrix of the predictions vs reference class... |
| compare_selected_features_barplot | plot the counts of the selected genes though samples colored... |
| deg_deseq2 | Select diffentially expressed genes(DGEs) from a DESeqDataSet... |
| deg_voom | Select diffentially expressed genes(DGEs) from a voom object |
| eliminate_glm | Eliminate features with glmnet |
| eliminate_RF | Eliminate features with Random forest by sorting variable... |
| filter0 | Basic filter which just removes very low expressed genes or... |
| filter_cpm | filter low expressed genes using cpm |
| filter_linear_correlation | filter genes by linear correlation with the class variable |
| filter_step | Stepwise feature selection |
| fit_glm | fit a glmnet model |
| fit_rf | fit a random forest model |
| fit_svmLinear | fit a svmLinear |
| fit_svmRadial | fit a svmRadial |
| get_class | Get class vector from the rse_gene |
| load_data | download an Rdata object from the recount2 project to be... |
| normalize_deseq2 | Normalize counts matrix with DESeq2 |
| normalize_voom | Normalize counts matrix with voom |
| pca | Plot top four principle components in a counts matrix colored... |
| plot_multipe_rocs | plot ROC curves from all models |
| tidyClass | Clean a class vector by keeping only alphabetical letters to... |
