Profile RNA-Seq Data Using TB Pathway Signatures

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Documentation for package ‘TBSignatureProfiler’ version 1.20.0

• 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.