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

This function computes prediction for 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, it will 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

re <- evaluateOriginalModel(input = TB_indian,
                            geneSignaturesName = c("Anderson_42"),
                            useAssay = "counts")
#> 
  |                                                                            
  |                                                                      |   0%
#> Now Evaluating: Anderson_42
#> 
  |                                                                            
  |======================================================================| 100%
#> 
re$Anderson_42_OriginalModel
#>  [1]  65989  34500  39793  74630  10202  44221  84480  18714  79863  38968
#> [11]  40546  45122 102946   7050  35734  37570  18867  10594  15629  11122
#> [21]  18156  15965  19055  11531  11702  24595  18539  18132   9670  12729
#> [31]  13905  21581  87043  13028  14255  10970  14128  37756  52082  17902
#> [41]  25673  72461  55514  12556