dot-OriginalModel_NoRetraining: TB gene signatures that do not require retraining.

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

TB gene signatures that do not require retraining.

Description

A function to obtain predicted score for TB gene signatures that do not need to be retrained.

Usage

.OriginalModel_NoRetraining(input, useAssay, geneSignaturesName, 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, it will run all available gene signatures' original models.
BPPARAM	An instance inherited from bplapply.

Details

Anderson_42 and Anderson_OD_51 used difference of sums to calculate prediction scores. Difference of sums is obtained by subtracting the sum of the expression of genes within signatures that are down-regulated from the sum of the expression of genes that are up-regulated within signatures. Kaforou_27, Kaforou_OD_44, and Kaforou_OD_53 used difference of arithmetic means to calculate prediction scores. Sweeney_OD_3 used difference of arithmetic mean to calculate prediction score.

Value

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

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