plotFragmentSizeDistributionEstimate: Estimate and plot Fragment Size Distribution.

Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/rw2collectqc.r

Description

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

Usage

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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 [email protected]

See Also

See vignettes: browseVignettes("ramwas").

Examples

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# 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)

ramwas documentation built on Oct. 31, 2019, 2:11 a.m.