saga_sampling: Sample preparation of the joint SAGA data set.

In mytalbot/saga_package: Surrogate Assay for Genotoxicity Assessment Package for Array Transformation Predictions

Description

saga_sampling will prepare training and testing data of the joint SAGA data set. An internal process is used to filter all data for candidate probes suited for classification of array data into transforming/untransforming. The list cannot be changed in this version and the package is optimized for this specific gene set. Also, a PCA plot may be generated to monitor the generalized context of the sample data within the SAGA training set.

Usage

saga_sampling(matrix.SAGA, matrix.test)

Arguments

matrix.SAGA	Matrix with SAGA model data
matrix.test	Matrix with user sample or test data

Value

matrix.train normalized, probe-averaged and batch-corrected SAGA training data.

labels.train class labels (factors) for SAGA training data. Can either be "transforming" or "untransforming".

matrix.unknown matrix of sample data with array names as row names and probes as column names.

mytalbot/saga_package documentation built on Feb. 26, 2021, 3:41 a.m.