reduce: Extract functional normalized data according to filter data

In molepi/DNAmArray: Streamlined workflow for the quality control, normalization and bias-free analysis of Illumina methylation array data - The Leiden approach

Extract functional normalized data according to filter data

Description

Extract functional normalized data according to filter data

Usage

reduce(
  GRset,
  RGset,
  what = c("beta", "M"),
  cutp = 0.01,
  cutsamples = 0.95,
  cutcpgs = 0.95,
  verbose = TRUE,
  ...
)

Arguments

GRset	'GenomicRatioSet' output from functional normalization
RGset	'RGset' output from filtering
what	return type either M- or beta-values
cutp	detection p-value threshold
cutsamples	threshold removing samples
cutcpgs	threshold removing probes
verbose	Default is TRUE
...	optional arguments getBeta

Details

Since functional normalization doesn't accept NA e.g. after probe filter the normalized 'GenomicRatioSet' and filtered 'RGChannelSet' need to be merged. Additionally if M-values are calculated we set -/+Inf values to +/-16 more details

Value

matrix with M- or beta-values

Author(s)

mvaniterson

molepi/DNAmArray documentation built on Aug. 24, 2022, 1:42 p.m.