getAnnotations: getAnnotations

Description Usage Arguments Value Methods (by class) Author(s) Examples

Description

getAnnotations

Usage

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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)

Author(s)

Alicia Schep

Examples

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# 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))

chromVAR documentation built on Nov. 8, 2020, 6:46 p.m.