plotFragmentSizeDistributionEstimate: Estimate and plot Fragment Size Distribution.

In andreyshabalin/ramwas: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

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 [e-mail]

See Also

See vignettes: browseVignettes("ramwas").

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)

andreyshabalin/ramwas documentation built on Sept. 27, 2021, 7:25 p.m.