Profile RA-Seq Data Using TB Pathway Signatures

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Documentation for package ‘TBSignatureProfiler’ version 0.99.29

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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.
deseq2_norm_rle Normalize gene expression count data.
distinctColors Generate a distinct palette for coloring different clusters.
LOOAUC_simple_multiple_noplot_one_df Perform Leave-one-out CV with Logistic Regression.
mkAssay Add SummarizedExperiment assays to the data structure.
plotQuantitative Create a boxplot using logistic regression and bootstrap LOOCV to evaluate signatures.
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.
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.
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.