AnnotatedVariants-class: Class "AnnotatedVariants"

In R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

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"]]

R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.