facopy (version 1.6.0)

addFeatures: 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.

Examples

data(myStudy) # load example study

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