rnb.execute.dreduction {RnBeads} | R Documentation |
Performs principal component analysis (PCA) and multi-dimensional scaling (MDS) of the samples in the given methylation dataset.
rnb.execute.dreduction(rnb.set, target = "sites")
rnb.set |
Methylation dataset as an object of type inheriting |
target |
|
Row names in the returned matrices are sample identifiers, determined based on the package option
"identifiers.column"
. See RnBeads Options for more information on this option.
Results of the dimension reduction in the form of a list with the following elements:
pca
Results of the PCA as returned by the function prcomp
.
mds
List of two elements - "manhattan"
and "euclidean"
, each of which is a
two-column matrix
storing the coordinates of the samples in a two-dimensional space. The
matrices are computed using the function isoMDS
.
Yassen Assenov
rnb.run.exploratory
for running the whole exploratory analysis module
library(RnBeads.hg19) data(small.example.object) regs <- c("sites", summarized.regions(rnb.set.example)) dreduction <- function(x) rnb.execute.dreduction(rnb.set.example, x) pcoordinates <- lapply(regs, dreduction) names(pcoordinates) <- regs str(pcoordinates)