estimateFragmentCenters: estimate center of fragments

In MMDiff2: Statistical Testing for ChIP-Seq data sets

Description

This function computes average shifts between forward and reverse strand and applies it to estimate fragment centers.

Usage

estimateFragmentCenters(MD, shift = NULL, draw.on = FALSE)

Arguments

MD	DBAmmd Object. This Object can be created using DBAmmd().
shift	can be set if the offset between forward and reverse strand is known (e.g. 1/2 median fragment size). In this case shift will not be estimated (DEFAULT: NULL)
draw.on	plot scatterplots for counts on forward vs reverse strand and histograms of determined shifts (DEFAULT: FALSE)

Value

DBAmmd object with updated slots Reads and MetaData.

See Also

DBAmmd, getPeakReads, compHists

Examples

## Example using a small data set provided with this package

data("MMD")
MMD.1 <- estimateFragmentCenters(MMD)

# To access centers of fragments:
Reads.C <- Reads(MMD.1,'Center')

# To access the determined shifts for each sample:
meta <- metaData(MMD.1)
meta$AnaData$Shifts

MMDiff2 documentation built on Nov. 8, 2020, 11:03 p.m.