AKSmooth: AKSmooth, locally kernel smoothing bisulfite sequencing data

In Junfang/AKSmooth: AKSmooth

Description

Modified nadaraya-watson kernel smoother with different kernel functions for the bisulfite sequencing data, which performs smoothing on low-coverage methylation data chromosome-wise.

Usage

AKSmooth(bsdata, h, kernel = c("Gaussian", "Epanechnikov", "Tricube"))

Arguments

bsdata	Bisulfite sequencing data containing genomic positions, read coverage and beta methylation values.
h	The smoothing window size.
kernel	The kernel function used for smoothing.

Details

bsdata is a data.frame contains 1.) genomic location, 2.) the chromosomal position, 3.) M values, describing the number of methylated read covering a single CpG, 4.) Cov values (read coverage), describing the total number of reads covering a single CpG, 5.) meth values, describing the beta estimated methylation values computed by M/Cov.

Value

The estimated DNA methylation value for a single sample.

Author(s)

Junfang Chen, Pavlo Lutsik and Ruslan Akulenko.

Examples

## load the bisulfite sequencing data (chromosome 21 for one single sample)
data(bn1chr21)
## define a bandwidth of 30 CpGs
fitChr21gau <- AKSmooth(bn1chr21, 30, "Gaussian")

Junfang/AKSmooth documentation built on May 14, 2019, 2:36 p.m.