R: getAnnotations

getAnnotations {chromVAR}

R Documentation

getAnnotations

Description

getAnnotations

Usage

getAnnotations(annotations, ...)

## S4 method for signature 'GRangesList'
getAnnotations(annotations, rowRanges, ...)

## S4 method for signature 'MatrixOrmatrix'
getAnnotations(annotations, ...)

## S4 method for signature 'data.frame'
getAnnotations(annotations, ...)

## S4 method for signature 'list'
getAnnotations(annotations, npeaks = NULL, ...)

## S4 method for signature 'character'
getAnnotations(annotations, rowRanges, column = NULL,
  ...)

Arguments

`annotations`	matrix, Matrix, or data.frame of fragment counts, or SummarizedExperiment with counts assays, see details
`...`	additional arguments to pass to SummarizedExperiment
`rowRanges`	GenomicRanges or GenomicRangesList or RangedSummarizedExperiment
`npeaks`	number of peaks
`column`	column of bed file with annotation names, see details

Value

SummarizedExperiment object with 'matches' assay

Methods (by class)

GRangesList: get annotation matrix from GRangesList
MatrixOrmatrix: get annotation matrix from Matrix or matrix
data.frame: get annotation matrix from data.frame
list: get annotation matrix from list
character: get annotations from bed files

Author(s)

Alicia Schep

Examples


# First get example counts
data(mini_counts, package = "chromVAR")

# Get annotations from genomic ranges list
library(GenomicRanges)
library(SummarizedExperiment)
my_annotation_granges <- GRangesList(GRanges("chr1", 
                                             ranges = IRanges(start = 
                                             c(566763,805090), width = 8)),
                                     GRanges("chr1", ranges = IRanges(start =
                                               c(566792,895798), width = 8)))
anno_ix <- getAnnotations(my_annotation_granges, 
                           rowRanges = rowRanges(mini_counts))

[Package chromVAR version 1.0.2 Index]