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