getAnnotations: getAnnotations

In GreenleafLab/chromVAR: Chromatin Variation Across Regions

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))

GreenleafLab/chromVAR documentation built on Aug. 20, 2019, 11:39 a.m.