computeWeightedDeviations: computeWeightedDeviations

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

Description

Computes weighted deviations in chromatin accessibility across sets of weights where the number of the annotation meaningful.

Usage

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computeWeightedDeviations(object, weights, ...)


  ## S4 method for signature 'SummarizedExperiment,SummarizedExperiment'
computeWeightedDeviations(object,
  weights, background_peaks = getBackgroundPeaks(object),
  expectation = computeExpectations(object))

## S4 method for signature 'SummarizedExperiment,Matrix'
computeWeightedDeviations(object,
  weights, background_peaks = getBackgroundPeaks(object),
  expectation = computeExpectations(object))

## S4 method for signature 'SummarizedExperiment,matrix'
computeWeightedDeviations(object,
  weights, background_peaks = getBackgroundPeaks(object),
  expectation = computeExpectations(object))

Arguments

object

chromVARCounts object

weights

chromVARweights object

...

additional arguments

background_peaks

(optional) background peaks matrix computed using getBackgroundPeaks, computed internally with default paramaters if not provided

expectation

(optional) expectations computed using computeExpectations, computed automatically if not provided

Details

multiprocessing using bplapply

Value

chromVARDeviations-class, which inherits from SummarizedExperiment, and has two assays: deviations and deviation scores.

Methods (by class)

Author(s)

Caleb Lareau

Examples

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# Register BiocParallel
BiocParallel::register(BiocParallel::SerialParam())
# Load very small example counts (already filtered)
data(mini_counts, package = "chromVAR")
# Load mini weighted counts
rdsA<-paste0(system.file('rds',package='gchromVAR'),'/mini_w.rds')
w_se <- readRDS(rdsA)

# Build weights from .bed file
files <- list.files(system.file('extdata',package='gchromVAR'),
         full.names = TRUE, pattern = "*.bed$")
data(mini_counts, package = "chromVAR")
uk_se <- importBedScore(SummarizedExperiment::rowRanges(mini_counts), files)

wdev <- computeWeightedDeviations(mini_counts, w_se)
ukdev <- computeWeightedDeviations(mini_counts, uk_se)

caleblareau/gchromVAR documentation built on Dec. 25, 2017, 5:46 a.m.