View source: R/IlluminaMethylationAnnotation-class.R
getAnnotation | R Documentation |
These functions access provided annotation for various Illumina methylation objects.
getAnnotation(object, what = "everything", lociNames = NULL,
orderByLocation = FALSE, dropNonMapping = FALSE)
getLocations(object, mergeManifest = FALSE,
orderByLocation = FALSE, lociNames = NULL)
getAnnotationObject(object)
getSnpInfo(object, snpAnno = NULL)
addSnpInfo(object, snpAnno = NULL)
dropLociWithSnps(object, snps = c("CpG", "SBE"), maf = 0, snpAnno = NULL)
getProbeType(object, withColor = FALSE)
getIslandStatus(object, islandAnno = NULL)
object |
A |
what |
Which annotation objects should be returned? |
lociNames |
Restrict the return values to these loci. |
orderByLocation |
Should the return object be ordered according to genomic location. |
dropNonMapping |
Should loci that do not have a genomic location
associated with it (by being marked as |
mergeManifest |
Should the manifest be merged into the return object? |
snpAnno |
The snp annotation you want to use; |
withColor |
Should the return object have the type I probe color labelled? |
snps |
The type of SNPs used. |
maf |
Minor allelle fraction. |
islandAnno |
Like |
getAnnotation
returns requested annotation as a
DataFrame
, with each row corresponding to a methylation loci.
If object
is of class IlluminaHumanAnnotation
no
specific ordering of the return object is imposed. If, on the other
hand, the class of object
imposes some natural order on the
return object (ie. if the object is of class
[Genomic](Methyl|Ratio)Set
), this order is kept in the return
object. Note that RGChannelSet
does not impose a specific
ordering on the methylation loci.
getAnnotationObject
returns the annotation object, as opposed
to the annotation the object contains. This is useful for printing
and examining the contents of the object.
getLocations
is a convenience function which returns
Locations
as a GRanges
and which furthermore drops
unmapped loci. A user should not need to call this function, instead
mapToGenome
should be used to get genomic coordinates and
granges
to return those coordinates.
getSnpInfo
is a conevnience function which gets a SNP DataFrame
containing information on which probes contains SNPs
where. addSnpInfo
adds this information to the rowRanges
or granges
of the object. dropLociWithSnps
is a
convenience function for removing loci with SNPs based on their MAF.
To see which options are available for what
, simply print the
annotation object, possibly using getAnnotationObject
.
For getAnnotation
, a DataFrame
with the requested
information.
For getAnnotationObject
, a IlluminaMethylationAnnotation
object.
For getLocations
, a GRanges
with the locations.
For getProbeType
and getIslandStatus
, a character
vector with the requested information.
For getSnpInfo
, a DataFrame
with the requested
information. For addSnpInfo
, an object of the same class as
object
but with the SNP information added to the metadata columns
of the granges of the object.
For dropLociWithSnps
an object of the same kind as the input,
possibly with fewer loci.
Kasper Daniel Hansenkhansen@jhsph.edu
IlluminaMethylationAnnotation
for the basic class,
mapToGenome
for a better alternative (for users) to
getLocations
.
if(require(minfiData)) {
table(getIslandStatus(MsetEx))
getAnnotation(MsetEx, what = "Manifest")
}
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