wideMetaProfile: Advanced usage: Meta Profile in wide format

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

Description

Calculates the wide-format meta profile, with regions in rows and positions in columns.

Usage

wideMetaProfile(sites, forward, reverse = NULL, upstream = 100,
  downstream = 100)


  ## S4 method for signature 
## 'GenomicRanges,BigWigFile_OR_RleList,NULL_OR_missing'
wideMetaProfile(sites,
  forward, reverse = NULL, upstream = 100, downstream = 100)


  ## S4 method for signature 
## 'GenomicRanges,BigWigFile_OR_RleList,BigWigFile_OR_RleList'
wideMetaProfile(sites,
  forward, reverse = NULL, upstream = 100, downstream = 100)

Arguments

sites	GenomicRanges: Single-bp genomic locations to calculate the meta-profile over.
forward	BigWigFile or RleList: Genome-wide signal stored either on disk as a BigWig-file or in memory as an RleList-object.
reverse	BigWigFile, RleList or NULL: If reverse=NULL, the forward signal is taken as unstranded. If not the genomic signal is taken to be stranded. The class of reverse must be the same as forward.
upstream	integer: Number of bases to extend upstream.
downstream	integer: Number of bases to extend downstream

Value

if reverse=NULL a matrix, else a list of two matrices with names "sense" and "anti"

Examples

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

enhancers <- subset(CAGE_clusters, clusterType == "enhancer")

# Unstranded data gives a single matrix:
wideMetaProfile(sites=enhancers,
                forward=CAGE_plus$WT)

# Stranded data gives two matrices (sense and anti):
wideMetaProfile(sites=enhancers,
                forward=CAGE_plus$WT,
                reverse=CAGE_minus$WT)

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