calcPhenotype: Calculates phenotype from microarray data.

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

This function uses ridge regression to calculate a phenotype from an gene expression, given a gene expression matrix where the phenotype is already known. The function also integrates the two datasets using a user-defined procedure, power transforms the known phenotype and provides several other options for flexible and powerful prediction from a gene expression matrix.

Usage

calcPhenotype(
  trainingExprData,
  trainingPtype,
  testExprData,
  batchCorrect = "eb",
  powerTransformPhenotype = TRUE,
  removeLowVaryingGenes = 0.2,
  minNumSamples = 10,
  selection = -1,
  printOutput = TRUE,
  removeLowVaringGenesFrom = "homogenizeData"
)

Arguments

trainingExprData	The training data. A matrix of expression levels, rows contain genes and columns contain samples, "rownames()" must be specified and must contain the same type of gene ids as "testExprData"
trainingPtype	The known phenotype for "trainingExprData". A numeric vector which MUST be the same length as the number of columns of "trainingExprData".
testExprData	The test data where the phenotype will be estimted. It is a matrix of expression levels, rows contain genes and columns contain samples, "rownames()" must be specified and must contain the same type of gene ids as "trainingExprData".
batchCorrect	How should training and test data matrices be homogenized. Choices are "eb" (default) for ComBat, "qn" for quantiles normalization or "none" for no homogenization.
powerTransformPhenotype	Should the phenotype be power transformed before we fit the regression model? Default to TRUE, set to FALSE if the phenotype is already known to be highly normal.
removeLowVaryingGenes	What proportion of low varying genes should be removed? 20 percent be default
minNumSamples	How many training and test samples are requried. Print an error if below this threshold
selection	How should duplicate gene ids be handled. Default is -1 which asks the user. 1 to summarize by their or 2 to disguard all duplicates.
printOutput	Set to FALSE to supress output
removeLowVaringGenesFrom	what kind of genes should be removed

Value

A vector of the estimated phenotype, in the same order as the columns of "testExprData".

Author(s)

Paul Geeleher, Nancy Cox, R. Stephanie Huang

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.