Description Usage Arguments Details Value Author(s)
View source: R/MT_process_meth.R
An RGChannelSet object is preprocessed, mapped to the genome and annotated by the respective annotation package.
1 2 3 4 5 6 7 8 9 10 | process_meth(
RGset,
projectfolder = "MT",
projectname = NULL,
preprocessing = c("illumina", "swan"),
addAnno = T,
SNPloci2drop = c("CpG", "SBE"),
MAF2drop = 0,
return.EpiSNPs.only = F
)
|
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 |
addAnno |
logical. If TRUE, annotation data is added from annotation package. |
SNPloci2drop |
character with SNP types, either |
MAF2drop |
numeric with minimum minor allele frequency of SNPs to drop if |
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). |
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.
GenomicRatioSet (containing Beta and M-values)
Frank Ruehle
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