evaluateOriginalModel: A function that implements the original methods for multiple...

In compbiomed/TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

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

Description

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")
re$Anderson_42_OriginalModel

compbiomed/TBSignatureProfiler documentation built on Oct. 29, 2024, 6:07 a.m.