assign.cv.output: Cross validation output

In compbiomed/ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

Cross validation output

Description

The assign.cv.output function outputs the summary results and plots for the cross validation done on the training dataset.

Usage

assign.cv.output(
  processed.data,
  mcmc.pos.mean.trainingData,
  trainingData,
  trainingLabel,
  adaptive_B = FALSE,
  adaptive_S = FALSE,
  mixture_beta = TRUE,
  outputDir
)

Arguments

processed.data	The list object returned from the assign.preprocess function.
mcmc.pos.mean.trainingData	The list object returned from the assign.mcmc function. Notice that for cross validation, the Y argument in the assign.mcmc function should be set as the training dataset.
trainingData	The genomic measure matrix of training samples (i.g., gene expression matrix). The dimension of this matrix is probe number x sample number. The default is NULL.
trainingLabel	The list linking the index of each training sample to a specific group it belongs to.
adaptive_B	Logicals. If TRUE, the model adapts the baseline/background (B) of genomic measures for the test samples. The default is FALSE.
adaptive_S	Logicals. If TRUE, the model adapts the signatures (S) of genomic measures for the test samples. The default is FALSE.
mixture_beta	Logicals. If TRUE, elements of the pathway activation matrix are modeled by a spike-and-slab mixture distribution. The default is TRUE.
outputDir	The path to the directory to save the output files. The path needs to be quoted in double quotation marks.

Details

The assign.cv.output function is suggested to run after the assign.preprocess, assign.mcmc and assign.summary function. For the cross validation, The Y argument in the assign.mcmc function is the output value "trainingData_sub" from the assign.preprocess function.

Value

The assign.cv.output returns one .csv file containing one/multiple pathway activity for each individual training samples, scatter plots of pathway activity for each individual pathway in all the training samples, and heatmap plots for the gene expression signatures for each individual pathways.

Author(s)

Ying Shen

Examples

assign.cv.output(processed.data=processed.data,
                 mcmc.pos.mean.trainingData=mcmc.pos.mean,
                 trainingData=trainingData1,
                 trainingLabel=trainingLabel1,
                 adaptive_B=FALSE, adaptive_S=FALSE,
                 mixture_beta=TRUE, outputDir=tempdir)

compbiomed/ASSIGN documentation built on June 28, 2023, 4 a.m.