addFeatures {facopy} | R Documentation

## Add Feature Annotation

### Description

Adds feature annotation to a `facopyInfo` object and calculates the overlapping frequency in the sample set for every combination of copy number and feature.

### Usage

    addFeatures(fad, what = c("ensembl", "cancergene", "oncogene",
                              "tumorsupressor", "lincRNA", "mirnas")[1],
                genome = c("hg18", "hg19", "mm8")[1],
                lMargin = 0, rMargin = 0, minoverlap = 1,
                data = NULL)

### Arguments

`fad` | `facopyInfo` object with a certain study's `facopy` data. Variable information should have been added beforehand on this object (see `addVariables`).
`what` | A character indicating the name of the feature set to use in subsequent analyses. If the name belongs to a set of features integrated in `facopy`, annotation is automatically loaded and the parameter `data` is not used.
`genome` | Reference genome build used in the copy number calling step prior to running `facopy`. Some feature sets may not be available depending on the selected genome.
`lMargin` | Number of base pairs with which to expand the left flanking side of each feature, increasing its chance to overlap alterations.
`rMargin` | Number of base pairs with which to expand the right flanking side of each feature, increasing its chance to overlap alterations.
`minoverlap` | Minimum overlap, in base pairs, between each feature and alteration.
`data` | If the genomic features of interest are not integrated within `facopy`, their information can be manually loaded using this parameter. Either a character or a `data.frame`. If a character, it indicates the file with the information, with headers and tab-delimited. In either case, the information shoul follow a structure with the following columns: - `chr` Chromosome in which the genomic feature lies. - `bp_st` Starting genomic position of the feature within the arm. - `bp_en` Ending genomic position of the feature within the arm. - `feature` Name of the feature. - `chr_q_arm` Chromosome arm in which the feature lies.

### Value

`facopyInfo` object with information on both variable and feature annotations.

### Author(s)

David Mosen-Ansorena

### Examples

    data(myStudy) # load example study

    myStudy = addFeatures(myStudy, "oncogene", "hg18")

[Package facopy version 1.13.0 Index]