AnnotateExtra-ExomeDepth-method: AnnotateExtra
In ExomeDepth: Calls Copy Number Variants from Targeted Sequence Data

AnnotateExtra,ExomeDepth-method

R Documentation

AnnotateExtra

Description

Add annotations to a ExomeDepth object.

Usage

## S4 method for signature 'ExomeDepth'
AnnotateExtra(x, reference.annotation, min.overlap = 0.5, column.name)

Arguments

`x`	An `ExomeDepth` object.
`reference.annotation`	The list of reference annotations in GRanges format.
`min.overlap`	Numeric, defaults to 0.5. This defines the minimum fraction of the CNV call that is covered by the reference call to declare that there is a significant overlap.
`column.name`	The name of the column used to store the overlap (in the slot CNV.calls).

Details

This function takes annotations in the GRanges format and adds these to the CNV calls in the ExomeDepth object. Note that a recent version of GenomicRanges (> 1.8.10) is required. Otherwise the function will return a warning and not update the ExomeDepth object.

Value

An ExomeDepth object with the relevant annotations added to the CNVcalls slot.

Examples


data(ExomeCount)  #pick an example count file
small_count <- ExomeCount[1:100, ]  #reduce the size for speedy computations
## create a dummy test object
example_object <- new('ExomeDepth', test = small_count$Exome2, reference = small_count$Exome3)

## artifically create a couple of CNV calls for this test
example_object@CNV.calls <- data.frame(chromosome = c(1,7),
                                       start = c(108778622, 61286538),
                                       end = c(109000909,61296735))

data(Conrad.hg19)
print(example_object@CNV.calls)
example_object_annotated <- AnnotateExtra(x = example_object,
                             reference.annotation = Conrad.hg19.common.CNVs,
                             min.overlap = 0.1,
                             column.name = 'Conrad.hg19')
print(example_object_annotated@CNV.calls)

ExomeDepth documentation built on Nov. 3, 2022, 5:05 p.m.