evaluateOriginalModel {TBSignatureProfiler} | R Documentation

## A function that implements the original methods for multiple TB signatures.

### Description

This function computes prediction foot multiple TB signatures based on their training models/methods. To avoid naming issues, the gene names for both training data and input gene sets have been updated using the `checkGeneSymbols`. TB signatures with available original models are: Anderson_42, Anderson_OD_51, Kaforou_27, Kaforou_OD_44, Kaforou_OD_53, Sweeney_OD_3, Maertzdorf_4, Verhagen_10, Jacobsen_3, Sambarey_HIV_10, Leong_24, Berry_OD_86, Berry_393, Bloom_OD_144, Suliman_RISK_4, Zak_RISK_16, Leong_RISK_29, and Zhao_NANO_6. The predicted score for each signature has been stored in the column data section of the input SummarizedExperiment study.

### Usage

    evaluateOriginalModel(
      input,
      geneSignaturesName,
      useAssay = 1,
      adj = 0.001,
      BPPARAM = BiocParallel::SerialParam(progressbar = TRUE)
    )

### Arguments

`input` | A SummarizedExperiment object with gene symbols as the assay row names.
`geneSignaturesName` | A character string/vector specifying the signature of interest. If `any(geneSignaturesName == "") == TRUE` run all available gene signatures' original models.
`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`.
`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`.

### Value

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

### Examples

    data("TB_hiv", package = "TBSignatureProfiler")
    re <- evaluateOriginalModel(input = TB_hiv,
    geneSignaturesName = c("Anderson_42", "Maertzdorf_15"), useAssay = "counts")
    re$Anderson_42_OriginalModel

[Package TBSignatureProfiler version 1.4.11 Index]