seeCov {DExMA} | R Documentation |
It uses the prince and prince.plot function from the swamp package to visualiza the effect of covariates in data variability
seeCov(expressionMatrix, pheno)
expressionMatrix |
A matrix or data frame with genes in rows and samples in columns. An ExpressionSet object can be used too |
pheno |
A dataframe with samples in rows and covariates in colums. It should contain only the most important covariates |
A visualization (heatmap) in which it can be seen how the data variability is affected by the covariates. The plot represents the p-values of each principal component associated with the covariates.
Requires the package swamp
Juan Antonio Villatoro Garcia, juanantoniovillatorogarcia@gmail.com
Martin Lauss (2019). swamp: Visualization, Analysis and Adjustment of High-Dimensional Data in Respect to Sample Annotations. R package version 1.5.1. https://CRAN.R-project.org/package=swamp
data(DExMAExampleData) seeCov(listMatrixEX$Study2, listPhenodatas$Study2)