Get the annotation(names) of bins in a SNPhood object.

Description

annotationBins2 is a helper function that returns annotation of the bins that are defined in the SNPhood object.

Usage

annotationBins2(SNPhood.o, regions = NULL, fullAnnotation = FALSE,
  verbose = TRUE)

Arguments

Value

If fullAnnotation is set to TRUE, a data.frame with the full annotation of the bins for the(subset of) SNP regions is returned. Otherwise, a character vector with only the annotation of the bins is returned.

Warning

The number of returned bins can easily be very large, in the order of millions. Be careful because the memory consumption due the resulting object may increase considerably. Reduce memory requirements by returning only a subset of SNP regions

Examples

data(SNPhood.o, package="SNPhood")
annotation.df  = annotationBins2(SNPhood.o, regions = 1:10, fullAnnotation = TRUE)
annotation.vec = annotationBins2(SNPhood.o, regions = 1:10, fullAnnotation = FALSE)

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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> 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/annotationBins2.Rd_%03d_medium.png", width=480, height=480)
> ### Name: annotationBins2
> ### Title: Get the annotation(names) of bins in a _SNPhood_ object.
> ### Aliases: annotationBins2
> 
> ### ** Examples
> 
> data(SNPhood.o, package="SNPhood")
> annotation.df  = annotationBins2(SNPhood.o, regions = 1:10, fullAnnotation = TRUE)
Check object integrity and validity. For large objects, this may take some time. Use the function changeObjectIntegrityChecking to disable this check for the object.
 Finished execution using 1 cores.
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> annotation.vec = annotationBins2(SNPhood.o, regions = 1:10, fullAnnotation = FALSE)
Check object integrity and validity. For large objects, this may take some time. Use the function changeObjectIntegrityChecking to disable this check for the object.
 Finished execution using 1 cores.
 Execution time: 0 secs
 Finished execution using 1 cores.
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> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>