getAnnot: Get CpG annotation
In methylGSA: Gene Set Analysis Using the Outcome of Differential Methylation
Description
Usage
Arguments
Details
Value
References
Description
This function gets CpG IDs and their corresponding gene symbols.
Usage
1
Arguments
array.type
A string. Either "450K" or "EPIC". Default is "450K".
group
A string. "all", "body", "promoter1" or "promoter2".
Default is "all". If group = "body", only CpGs on gene body will be
pulled out. If group = "promoter1" or group = "promoter2",
only CpGs on promoters will be pulled out. Here is the definition of "body",
"promoter1" and "promoter2" according to the annotation in
IlluminaHumanMethylation450kanno.ilmn12.hg19 or
IlluminaHumanMethylationEPICanno.ilm10b4.hg19.
body: CpGs whose gene group correspond to "Body" or "1stExon"
promoter1: CpGs whose gene group correspond to "TSS1500" or "TSS200"
promoter2: CpGs whose gene group correspond to "TSS1500", "TSS200",
"1stExon", or "5'UTR".
If group = "all", all CpGs will be pulled out.
Details
The implementation of the function is modified
from .flattenAnn function in missMethyl package.
Value
A data frame contains CpG IDs and gene symbols.
References
Hansen KD (2016). IlluminaHumanMethylation450kanno.ilmn12.hg19:
Annotation for Illumina's 450k methylation arrays. R package version 0.6.0.
Hansen KD (2017). IlluminaHumanMethylationEPICanno.ilm10b4.hg19:
Annotation for Illumina's EPIC methylation arrays. R package version 0.6.0,
https://bitbucket.com/kasperdanielhansen/Illumina_EPIC.
Phipson B, Maksimovic J and Oshlack A (2015).
<e2><80><9c>missMethyl: an R package for analysing methylation data from
Illuminas HumanMethylation450 platform.<e2><80><9d> Bioinformatics, pp. btv560.
methylGSA documentation built on Nov. 8, 2020, 8:29 p.m.
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Description Usage Arguments Details Value References
Description
This function gets CpG IDs and their corresponding gene symbols.
Usage
1 |
Arguments
array.type |
A string. Either "450K" or "EPIC". Default is "450K". |
group |
A string. "all", "body", "promoter1" or "promoter2". Default is "all". If group = "body", only CpGs on gene body will be pulled out. If group = "promoter1" or group = "promoter2", only CpGs on promoters will be pulled out. Here is the definition of "body", "promoter1" and "promoter2" according to the annotation in IlluminaHumanMethylation450kanno.ilmn12.hg19 or IlluminaHumanMethylationEPICanno.ilm10b4.hg19.
If group = "all", all CpGs will be pulled out. |
Details
The implementation of the function is modified from .flattenAnn function in missMethyl package.
Value
A data frame contains CpG IDs and gene symbols.
References
Hansen KD (2016). IlluminaHumanMethylation450kanno.ilmn12.hg19: Annotation for Illumina's 450k methylation arrays. R package version 0.6.0.
Hansen KD (2017). IlluminaHumanMethylationEPICanno.ilm10b4.hg19: Annotation for Illumina's EPIC methylation arrays. R package version 0.6.0, https://bitbucket.com/kasperdanielhansen/Illumina_EPIC.
Phipson B, Maksimovic J and Oshlack A (2015). <e2><80><9c>missMethyl: an R package for analysing methylation data from Illuminas HumanMethylation450 platform.<e2><80><9d> Bioinformatics, pp. btv560.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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