MethTargetedNGS (version 1.4.0)

methEntropy: Calculate Methylation Entropy

Description

Entropy comparison between healthy and tumor samples can identify significant CpG sites which are contributing most in the tumor development either by hypomethylation or hypermethylation. Also such way can help in understanding the randomness in methylation status. Sliding window of 4 was used to calculate the entropy in the sample, which can analyze 16 different pattern for entropy calculation.

Usage

methEntropy(x)

Arguments

x

Matrix from methAlign. Also matrix where columns represents Cytosine of CpG sites and rows represents sequences

Value

Matrix containing entropy for every sequence and group of 4 cpg sites.

References

Xie, H., Wang, M., de Andrade, A., Bonaldo, M.d.F., Galat, V., Arndt, K., Rajaram, V., Goldman, S., Tomita, T. and Soares, M.B. (2011) Genome-wide quantitative assessment of variation in DNA methylation patterns. Nucleic Acids Research, 39, 4099-4108.

See Also

methAlign

Examples

healthy = system.file("extdata", "Healthy.fasta", package = "MethTargetedNGS")
reference = system.file("extdata", "Reference.fasta", package = "MethTargetedNGS")
methP <- methAlign(healthy,reference)
entMeth <- methEntropy(methP)
plot(entMeth,type="l")