.OriginalModel_NoRetraining | TB gene signatures that do not require retraining. |
.OriginalModel_Retraining | TB gene signatures that require retraining. |
addTBsignature | Introduce a new signature into the TBSignatureProfiler. |
bootstrapAUC | Bootstrap the AUC and conduct T-Tests for a collection of signatures. |
Bootstrap_LOOCV_LR_AUC | Bootstrap on Leave-one-out CV with Logistic Regression. |
common_sigAnnotData | Annotation information for published TB signatures. |
compareAlgs | Compare scoring algorithms on a single signature via heatmap or boxplot. |
compareBoxplots | Create a comparison plot of boxplots for bootstrapped AUC values. |
COVIDsignatures | A list of published/pre-print COVID-19 signatures. |
cv_glmnet_OriginalModel | Train original model for gene signatures Leong_24, Leong_RISK_29, Zhao_NANO_6 using lasso logistic regression. |
deseq2_norm_rle | Normalize gene expression count data. |
distinctColors | Generate a distinct palette for coloring different clusters. |
evaluateOriginalModel | A function that implements the original methods for multiple TB signatures. |
knn_OriginalModel | Train original model for gene signatures Berry_393 and Berry_OD_86. |
lda_OriginalModel | Train original model for gene signatures Jacobsen_3 and Sambarey_HIV_10. |
LOOAUC_simple_multiple_noplot_one_df | Perform Leave-one-out CV with Logistic Regression. |
mkAssay | Add SummarizedExperiment assays to the data structure. |
ObtainSampleScore_OriginalModel | Obtain training data, testing data, and train signature's original model. |
OriginalTrainingData | Discovery datasets for corresponding gene signatures. |
plotQuantitative | Create a boxplot using logistic regression and bootstrap LOOCV to evaluate signatures. |
randomForest_OriginalModel | Train original model for gene signatures Maertzdorf_4, Maertzdorf_15, Verhagen_10, and LauxdaCosta_OD_3. |
ref_combat_impute | A function for reference batch correction and imputation. |
runTBsigProfiler | Run TB gene signature profiling. |
sigAnnotData | Annotation information for published TB signatures. |
signatureBoxplot | Plot a boxplot of signature genes. |
signatureGeneHeatmap | Plot a heatmap of a single signature score with individual gene expression levels. |
signatureHeatmap | Plot a heatmap of signature scores. |
SignatureQuantitative | Use logistic regression and bootstrap LOOCV to evaluate signatures. |
signatureROCplot | Create an array of ROC plots to compare signatures. |
signatureROCplot_CI | Create an array of ROC plots with confidence interval bands to compare signatures. |
subsetGeneSet | Filter gene expression value matrix based on certain gene sets. |
SulimanOriginalModel | Train original model gene signature Suliman_RISK_4. |
svm_OriginalModel | Train original model for gene signatures Bloom_OD_144 and Zak_RISK_16. |
tableAUC | Create a table of results for t-tests and bootstrapped AUCs for multiple scored signatures. |
TBcommon | A list of published TB signatures, using author-given names. |
TBsignatures | A list of published TB signatures. |
TBsignaturesSplit | Up/Down-regulated genes information for selected TB signatures. |
TBSPapp | Run the TBSignatureProfiler Shiny application. |
TB_hiv | An example TB dataset with TB/HIV data. |
TB_indian | An example TB dataset with Indian population data. |