# Profile RNA-Seq Data Using TB Pathway Signatures

## Documentation for package ‘TBSignatureProfiler’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.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.