R: Estimate and plot Fragment Size Distribution.

plotFragmentSizeDistributionEstimate {ramwas}

R Documentation

Estimate and plot Fragment Size Distribution.

Description

RaMWAS functions for estimation and plotting of the fragment size distribution.

Usage

estimateFragmentSizeDistribution(frdata, seqLength)
plotFragmentSizeDistributionEstimate(      
        frdata,
        estimate,
        col1 = "blue",
        col2 = "red")

Arguments

`frdata`	Distribution of distances from the starts of isolated reads to the respective CpGs.
`seqLength`	The length of sequenced part of the fragments. The fragments are assument to not be smaller than `seqLength`.
`estimate`	Fragment size distribution estimate.
`col1`	Color of `frdata` points.
`col2`	Color of `estimate` curve.

Value

The function estimateFragmentSizeDistribution returns the estimate of the fragment size distribution.

Note

If the length of frdata is equal to seqLength, the fragments are assumed to all be of length seqLength.

Author(s)

Andrey A Shabalin andrey.shabalin@gmail.com

Examples

# Simulate data
x = 0:250
truemean = 1 - pnorm(x, mean = 150, sd = 50)
frdata = rpois(n = length(x), lambda = truemean*300)

# Estimate fragment size distribution
estimate = estimateFragmentSizeDistribution(frdata, seqLength = 50)

# Plot fragment size distribution estimate
plotFragmentSizeDistributionEstimate(frdata, estimate)

[Package ramwas version 1.6.0 Index]