AnnotatedVariants-class {R453Plus1Toolbox} | R Documentation

## 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"]]

[Package R453Plus1Toolbox version 1.30.0 Index]