ObtainSampleScore_OriginalModel: Obtain training data, testing data, and train signature's...
In dfjenkins3/TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

ObtainSampleScore_OriginalModel

R Documentation

Obtain training data, testing data, and train signature's original model.

Description

Obtain training data, testing data, and train signature's original model.

Usage

ObtainSampleScore_OriginalModel(
  theObject_train,
  useAssay,
  gene_set,
  input,
  SigName,
  obtainDiagnosis,
  annotationColName,
  FUN,
  adj
)

Arguments

`theObject_train`	A SummarizedExperiment object that has been pre-stored in the data file: OriginalTrainingData.
`useAssay`	A character string or an integer specifying the assay in the `input`. Used for the test SummarizedExperiment object. Default is 1, indicating the first assay in the test SummarizedExperiment object.
`gene_set`	A character vector that includes gene symbols for selected gene signature.
`input`	A SummarizedExperiment object with gene symbols as the assay row names.
`SigName`	Optional. A character string that indicates the name for `gene_set`. `SigName` is used to provide information when gene signatures were missing in the test data.
`obtainDiagnosis`	Boolean. Used to create training data if TRUE. Default is FALSE
`annotationColName`	A character string specifying the column name of disease status. Only used when creating training data. Default is NULL.
`FUN`	A character string specifying the function name of the corresponding signature's original model.
`adj`	A small real number used in combat to solve for genes with 0 counts in rare cases. Not required for most of cases.