meffil.methylation.pcs: Compute principal components of a methylation matrix.

In perishky/meffil: Efficient algorithms for DNA methylation

Compute principal components of a methylation matrix.

Description

Compute principal components of a methylation matrix.

Usage

meffil.methylation.pcs(
  beta,
  probe.range = 50000,
  sites = NULL,
  samples = NULL,
  autosomal = T,
  winsorize.pct = NA,
  outlier.iqr.factor = NA,
  full.obj = F,
  verbose = F
)

Arguments

beta	Output from meffil.normalize.samples(), either a matrix or a GDS filename.
probe.range	Default = 50000. How many probes to be used in calculating PCs.
sites	Subset of CpG sites to consider (row names of beta) (Default: NULL).
samples	Subset of samples to consider (column names of beta) (Default: NULL).
autosomal	If true, remove probes on sex chromosomes (Default: TRUE).
winsorize.pct	Apply to methylation levels winsorized to the given level. Set to NA to avoid winsorizing (Default: NA).
outlier.iqr.factor	Apply to methylation after setting, for each CpG site, values less than Q1 - outlier.iqr.factor * IQR or more than Q3 + outlier.iqr.factor * IQR to NA. Here IQR is the inter-quartile range of the methylation levels at the CpG site, i.e. Q3-Q1. Set to NA to skip this step (Default: NA).
full.obj	Default = FALSE. If true, then return the full prcomp object rather than just the PCs.
verbose=T	Print progress messages?

Value

the principal components of normalized.beta.

perishky/meffil documentation built on March 20, 2024, 1:56 a.m.