Class "AnnotatedVariants"

Description

A class for storing annotation about variants. An object of this class is returned by the method annotateVariants. The class has not been designed to be created by users directly.

Details

The list encapsulated by this class has one element for each variant. Each element is a nested list with the elements genes, transcripts, exons and snps. All these elements are data frames listing genes, transcripts, exons or snps respectively that were affected by the variant. Use the example below to explore the data frames' contents.

Objects from the Class

Objects can be created by calls of the form new("AnnotatedVariants"). The method annotateVariants returns AnnotatedVariants-objects.

Slots

annotatedVariants:

Object of class "list" with one entry for each variant.

Methods

annotatedVariants

signature(object = "AnnotatedVariants"): Get the list with variants.

annotatedVariants<-

signature(object = "AnnotatedVariants", value = "list"): Set a new list with variants.

names

signature(x = "AnnotatedVariants"): Get the names of the with variants.

names<-

signature(x = "AnnotatedVariants", value = "character"): Set the names of the variants.

Author(s)

Hans-Ulrich Klein

See Also

annotateVariants, htmlReport

Examples

variants = data.frame(
    start=c(106157528, 106154991,106156184),
    end=c(106157528, 106154994,106156185),
    chromosome=c("4", "4", "4"),
    strand=c("+", "+", "+"),
    seqRef=c("A", "ATAG", "---"),
    seqMut=c("G", "----", "ATA"),
    seqSur=c("TACAGAA", "TTTATAGATA", "AGC---TCC"),
    stringsAsFactors=FALSE)
rownames(variants) = c("snp", "del", "ins")
## Not run: av = annotateVariants(variants)
## Not run: annotatedVariants(av)[["snp"]]

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 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(R453Plus1Toolbox)
Loading required package: VariantAnnotation
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: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

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

    tabulate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/R453Plus1Toolbox/AnnotatedVariants-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: AnnotatedVariants-class
> ### Title: Class "AnnotatedVariants"
> ### Aliases: AnnotatedVariants-class annotatedVariants
> ###   annotatedVariants,AnnotatedVariants-method
> ###   annotatedVariants<-,AnnotatedVariants,list-method
> ###   names,AnnotatedVariants-method
> ###   names<-,AnnotatedVariants,character-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> variants = data.frame(
+     start=c(106157528, 106154991,106156184),
+     end=c(106157528, 106154994,106156185),
+     chromosome=c("4", "4", "4"),
+     strand=c("+", "+", "+"),
+     seqRef=c("A", "ATAG", "---"),
+     seqMut=c("G", "----", "ATA"),
+     seqSur=c("TACAGAA", "TTTATAGATA", "AGC---TCC"),
+     stringsAsFactors=FALSE)
> rownames(variants) = c("snp", "del", "ins")
> ## Not run: av = annotateVariants(variants)
> ## Not run: annotatedVariants(av)[["snp"]]
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>