process_meth: Preprocessing and annotation of methylation array data

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

An RGChannelSet object is preprocessed, mapped to the genome and annotated by the respective annotation package.

Usage

process_meth(
  RGset,
  projectfolder = "MT",
  projectname = NULL,
  preprocessing = c("illumina", "swan"),
  addAnno = T,
  SNPloci2drop = c("CpG", "SBE"),
  MAF2drop = 0,
  return.EpiSNPs.only = F
)

Arguments

RGset	RGChannelSet object with methylation data.
projectfolder	character with directory for output files (will be generated if not exisiting).
projectname	optional character prefix for output file names.
preprocessing	character with preprocessing procedures to apply. Any of "raw", "illumina", "swan". If multiple procedures are selected, the one with higest priority is used: "raw" < "illumina" < "swan". If "swan" is selected, at least one more procedure must be selected, too. If NULL, input object is expected to be already preprocessed.
addAnno	logical. If TRUE, annotation data is added from annotation package.
SNPloci2drop	character with SNP types, either "CpG" (SNPs overlapping the CpG site) and/or "SBE" (SNP at the single base extension of CpG-site). CpG sites overlapping these SNPs are removed from the dataset. If NULL, no CpG sites are removed.
MAF2drop	numeric with minimum minor allele frequency of SNPs to drop if SNPloci2drop is specified.
return.EpiSNPs.only	logical. If TRUE, the returned GenomicRatioSet contains only CpG-sites overlapping with SNP locations (usefull to focus on SNPs influencing methylation processes).

Details

This function takes an RGChannelSet as input and transforms it to a MethylSet object using one of 3 possible preprocessing procedures from minfi package:

• preprocessRaw (no normalisiation)

• preprocessIllumina applies background subtraction as well as control normalization like in Illumina Genome studio

• preprocessSWAN applies SWAN normalization (Subset quantile Within-Array Normalization) method on a preprocessed MethylSet to reduce the technical variability of Type I and Type II Illumina probes. For this, Illumina preprocessed MethylSet is used if given, the raw preprocessed MethylSet otherwise.

If no preprocessing is selected, the input object is expected to be already preprocessed. Next, the MethylSet object is mapped to the genome (Loci which cannot be mapped to a genomic position are dropped) and converted to a GenomicRatioSet. Finally, annotation data is added from the respective annotation package. CpG sites overlapping with SNPs optionally can be removed from the dataset. If these sites are of special interest, the returned GenomicRatioSet can be specified to contains these CpG-sites only.

Value

GenomicRatioSet (containing Beta and M-values)

Author(s)

Frank Ruehle

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.