Get the annotation of SNP regions for a SNPhood object.

Description

Return the annotation of the SNP regions that are defined in the SNPhood object.

Usage

annotationRegions(SNPhood.o, asGRangesObj = FALSE, verbose = FALSE)

Arguments

Value

If asGRangesObj is set to TRUE, a GRanges object is returned. Otherwise, a character vector with the currently stored SNP annotation is returned.

Examples

data(SNPhood.o, package="SNPhood")
IDs.vec = annotationRegions(SNPhood.o, asGRangesObj = FALSE)
IDs.gr  = annotationRegions(SNPhood.o, asGRangesObj = TRUE)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(SNPhood)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: data.table

Attaching package: 'data.table'

The following object is masked from 'package:GenomicRanges':

    shift

The following object is masked from 'package:IRanges':

    shift

Loading required package: checkmate

------------------------------------------------------------------------------------------------------------------
|       Welcome to the SNPhood package and thank you for using our software. This is SNPhood version 1.2.2.      |
| See the vignettes (type browseVignettes("SNPhood") or the help pages for how to use SNPhood for your analyses. |
|       Thank you for using our software. Please do not hesitate to contact us if there are any questions.       |
------------------------------------------------------------------------------------------------------------------

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SNPhood/annotationRegions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: annotationRegions
> ### Title: Get the annotation of SNP regions for a _SNPhood_ object.
> ### Aliases: annotationRegions
> 
> ### ** Examples
> 
> data(SNPhood.o, package="SNPhood")
> IDs.vec = annotationRegions(SNPhood.o, asGRangesObj = FALSE)
> IDs.gr  = annotationRegions(SNPhood.o, asGRangesObj = TRUE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>