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

meffil.methylation.pcsR Documentation

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 June 9, 2024, 5:59 p.m.