Profile RNA-Seq Data Using TB Pathway Signatures

[Up] [Top]

Documentation for package ‘TBSignatureProfiler’ version 1.4.0

Help Pages

.OriginalModel_NoRetraining TB gene signatures do not require retraining A function to obtain predicted score for TB gene signatures that do not need to be retrained.
.OriginalModel_Retraining TB gene signatures require retraining
addTBsignature Introduce a new signature into the TBSignatureProfiler
BerryOriginalModel Train original model for gene signatures: Berry_393 and Berry_OD_86
Bloom_Zak_OriginalModel Train original model for gene signatures Bloom_OD_144 and Zak_RISK_16
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.
deseq2_norm_rle Normalize gene expression count data.
distinctColors Generate a distinct palette for coloring different clusters.
evaluateOriginalModel A function that implements the original models for various TB signatures.
Jacobsen_Sambarey_OriginalModel Train original model for gene signatrues: Jacobsen_3 and Sambarey_HIV_10
LeongOriginalModel Train original model for gene signatures: Leong_24 and Leong_RISK_29
LOOAUC_simple_multiple_noplot_one_df Perform Leave-one-out CV with Logistic Regression.
Maertzdorf_Verhagen_daCosta_OriginalModel Train original model for gene signatures: Maertzdorf_4, Maertzdorf_15, Verhagen_10, and LauxdaCosta_OD_3
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 correpsonding gene signatures
plotQuantitative Create a boxplot using logistic regression and bootstrap LOOCV to evaluate signatures.
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 certatin gene sets.
SulimanOriginalModel Train original model gene signature Suliman_RISK_4
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.