affiXcanPca {AffiXcan} | R Documentation |
Perform a PCA on each experiment found in MultiAssayExperiment objects
affiXcanPca(tbaPaths, varExplained, scale, regionsCount, BPPARAM = bpparam())
tbaPaths |
A vector of strings, which are the paths to MultiAssayExperiment RDS files containing the tba values |
varExplained |
An integer between 0 and 100; varExplained=80 means that the principal components selected to fit the models must explain at least 80 percent of variation of TBA values |
scale |
A logical; if scale=FALSE the TBA values will be only centered, not scaled before performing PCA |
regionsCount |
An integer, that is the summation of length(assays()) of every MultiAssayExperiment RDS object indicated in the param tbaPaths; it is the returning value from overlookRegions() |
BPPARAM |
A BiocParallelParam object. Default is bpparam(). For details on BiocParallelParam virtual base class see browseVignettes("BiocParallel") |
pca: A list containing lists named as the MultiAssayExperiment::experiments() found in the MultiAssayExperiment objects listed in the param tbaPaths. Each of these lists contains two objects:
eigenvectors: A matrix containing eigenvectors for those principal components selected according to the param varExplained
pcs: A matrix containing the principal components values selected according to the param varExplained
if (interactive()) { tbaPaths <- system.file("extdata","training.tba.toydata.rds", package="AffiXcan") regionsCount <- overlookRegions(tbaPaths) pca <- affiXcanPca(tbaPaths=tbaPaths, varExplained=80, scale=TRUE, regionsCount=regionsCount) }