R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
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Results 1 - 6 of 6 found.
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getNearest (Package: FDb.InfiniumMethylation.hg18) : Annotate a group of probes supplied as a GenomicRanges object

This function encapsulates the common task of finding what gene/tx/tss is closest to a list of probes, as might be the case after a model fit.

● Data Source: BioConductor
● Keywords:
● Alias: getNearest, getNearestGene, getNearestTSS, getNearestTranscript
● 0 images

getPlatform (Package: FDb.InfiniumMethylation.hg18) : Retrieve annotations for HumanMethylation27 or HumanMethylation450 chips

FDb.InfiniumMethylation.hg19 is an omnibus package that merges all of the existing Illumina Infinium DNA methylation probe annotations into one FDb. However, most users will be analyzing one of the two chips at any given time. The utility functions getPlatform(platform), get450k(), and get27k() retrieve a compact GenomicRanges form of the annotations for the requested platform.

● Data Source: BioConductor
● Keywords:
● Alias: get27k, get450k, getPlatform
● 0 images

hg18.islands (Package: FDb.InfiniumMethylation.hg18) : CpG islands found by Wu, Irizarry, and Feinberg via hidden Markov model

This GRanges object was constructed from the data provided at http://rafalab.jhsph.edu/CGI/model-based-cpg-islands-hg18.txt

● Data Source: BioConductor
● Keywords: data
● Alias: hg18.islands
● 0 images

miscData (Package: FDb.InfiniumMethylation.hg18) : miscellaneous data used in the construction of this FeatureDb package

In the subdirectory inst/build/, there are several scripts that rebuild this FeatureDb from scratch. A handful of intermediate results from dbSNP and comparison of existing datasets are required to patch small gaps in the Illumina manifests. These datasets supply those intermediate results.

● Data Source: BioConductor
● Keywords: data
● Alias: SNPs.hg18, hg18ToHg19, hm27.SNP.colors, hm27.controls, hm450.controls, hm450k.rsProbes, unmappable
● 0 images

FDb.InfiniumMethylation.hg18 (Package: FDb.InfiniumMethylation.hg18) : Annotation package for Illumina Infinium DNA methylation probes

This package loads one or more FeatureDb objects. Such FeatureDb objects are an R interface to prefabricated databases contained by this package. In the case of the Infinium methylation FDb, it is FDb.InfiniumMethylation.hg18 (for the moment; hg18 may come later, or alternatively users can use liftOver() from rtracklayer to do it).

● Data Source: BioConductor
● Keywords: data, package
● Alias: FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg18-package
● 0 images

seqinfo.hg18 (Package: FDb.InfiniumMethylation.hg18) : Sequence names, lengths, and circularity for hg18

These avoid having to load a BSgenome package just to assign seqinfo(GR).

● Data Source: BioConductor
● Keywords: data
● Alias: seqinfo.hg18
● 0 images