dot-OriginalModel_NoRetraining: TB gene signatures that do not require retraining.
In dfjenkins3/TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

.OriginalModel_NoRetraining

R Documentation

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.