Create an RGChannelSet object from Illumina IDAT files and add phenotype data.
character with path to base directory containing IDAT files for all arrays.
dataframe with sample sheet or character with regular expression for identifying the corresponding sample sheet within the base directory or its subdirectories. If NULL, no sample information file is loaded.
Name of sample column in sample sheet
character with filepath to a covariates file if given. NULL otherwise.
character with name of sample column in (optional) covariates file.
This functions uses the
minfi package to load methylation data from Illumnia
Human Methylation 450k microarrays.
SampleSheetRegExp argument is NULL, the function finds all two-color IDAT files in the
directory given by
baseDir including all subdirectories. Two-color IDAT files consist of pairs of
files with names ending in
SampleSheetRegExp is not NULL,
the corresponding sample sheet is identified via regular expression (file must be located in base)
and all listed arrays are loaded.
Susequently, additional phenotype data given in
covarfile is added to the object.
methylation data classes (from
minfi manual) :
RGChannelSet: raw data from the IDAT files; this data is organized at the probe (not CpG locus) level. This data has two channels: Red and Green. This data type contains control probe data.
MethylSet: data organized by the CpG locus level, but not mapped to a genome. This data has two channels: Meth (methylated) and Unmeth (unmethylated).
RatioSet: data organized by the CpG locus level, but not mapped to a genome. The data has at least one of two channels: Beta and/or M (logratio of Beta). It may optionally include a CN channel (copy number).
GenomicMethylSet: like a MethylSet, but mapped to a genome.
GenomicRatioSet: like a RatioSet, but mapped to the genome.
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