evaluateOriginalModel {TBSignatureProfiler} | R Documentation |
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.
evaluateOriginalModel( input, geneSignaturesName, useAssay = 1, adj = 0.001, BPPARAM = BiocParallel::SerialParam(progressbar = TRUE) )
input |
A SummarizedExperiment object with gene symbols as the assay row names. |
geneSignaturesName |
A character string/vector specifying the signature
of interest. If |
useAssay |
A character string or an integer specifying the assay in the
|
adj |
A small positive real number used in |
BPPARAM |
An instance inherited from |
A SummarizedExperiment object with predicted scores for each sample obtained from the signature's original model.
data("TB_hiv", package = "TBSignatureProfiler") re <- evaluateOriginalModel(input = TB_hiv, geneSignaturesName = c("Anderson_42", "Maertzdorf_15"), useAssay = "counts") re$Anderson_42_OriginalModel