.OriginalModel_Retraining {TBSignatureProfiler} | R Documentation

## TB gene signatures that require retraining.

### Description

A function to obtain predicted score for TB gene signatures that need retraining of original models.

### Usage

    .OriginalModel_Retraining(input, useAssay, geneSignaturesName, adj, BPPARAM)

### Arguments

`input` | A SummarizedExperiment object with gene symbols as the assay row names.
`useAssay` | A character string or an integer specifying the assay in the `input`. Default is the first assay in the assay list. Used for the test SummarizedExperiment object. Default is `1`, indicating the first assay in the `input`.
`geneSignaturesName` | A character string/vector specifying the signature of interest. If `any(geneSignaturesName == "") == TRUE` run all available gene signatures' original models.
`adj` | A small positive real number used in `ComBat` to solve for genes with 0 counts(rare cases). Default is `1e-3`.
`BPPARAM` | An instance inherited from `bplapply`.

### Details

Maertzdorf_4 and Maertzdorf_15 were trained using random forest to distinguish patients with active TB from healthy controls. Verhagen_10 was also trained using random forest to distinguish samples with active TB from either latent infection or healthy controls. The random forest model was build using `randomForest`.
Jacobsen_3 were trained using linear discriminatory analysis (LDA) to distinguish samples with active TB from latent infection status. Sambarey_HIV_10 were also trained using LDA to distinguish samples with active TB from either latent infection, healthy control, or other disease (HIV). The LDA model was build using `lda`.
Berry_OD_86 and Berry_393 were trained using K-nearest neighbors (KNN) model to differentiate samples with active TB from latent infection status. The KNN model was build using `knn`.
Suliman_RISK_4 and Zak_RISK_16 were trained using support vector machines (SVM) to distinguish TB progressor from non-progressors. The input gene expression features for Suliman_RISK_4 used the paired ratio of GAS6/CD1C, SEPTIN4/BLK, SEPTIN4/CD1C, GAS6/BLK. The SVM model was build using `svm`.

### Value

A SummarizedExperiment object with predicted scores for each sample obtained from the signature's original model.

[Package TBSignatureProfiler version 1.4.11 Index]