agnosticImport: Advanced usage: Import chunks of a genome-wide vector

In MalteThodberg/TeMPO: Tidy Meta Profiles using Bioconductor and the Tidyverse

Description

Import regions from coverage stored as a BigWigFile or RleList and return a NumericList. Regions unkown to the BigWigFile/RleList will be ignored, and it is ensured the output vectors all have the same length.

Usage

agnosticImport(signal, sites)

## S4 method for signature 'BigWigFile,GenomicRanges'
agnosticImport(signal, sites)

## S4 method for signature 'RleList,GenomicRanges'
agnosticImport(signal, sites)

Arguments

signal	BigWigFile or RleList: Genomic signal
sites	GenomicRanges: Regions to be extracted

Value

NumericList

Examples

data("CAGE_clusters")
data("CAGE_plus")

# Import from an RleList
agnosticImport(signal=CAGE_plus$WT, sites=subset(CAGE_clusters, strand=="+"))

# Import from a BigWig
## Not run: 
library(AnnotationHub)
ah <- AnnotationHub()
DNase <- ah[["AH32877"]]
agnosticImport(signal=DNase, sites=subset(CAGE_clusters, strand=="+"))

## End(Not run)

MalteThodberg/TeMPO documentation built on May 15, 2019, 11:48 a.m.