FindCpGIslands: Highlighting all CpG Islands

In diannamcallister/MethylExpress: Visual investigation of physical characteristics of methylation of DNA

Description

A function that returns a visual output highlighting all CpG islands found in the DNA strand.

Usage

findCpGIslands(nucleotides)

Arguments

nucleotides

A string of nucleotides of a DNA sequence

Details

More details about how the CpG islands are calculated can be found in the the vignette, but a quick overview as to how nucleotides are considered part of a CpG islands is:

1. there must be at least 200 nucleotides in the sequence to observe

2. the number of CGs must be > 50% of the part of DNA being looked at

3. the observed number of CGs - to - expected number of CGs ratio must be > 60%

Value

A visual output of highlighted CpG Islands in the DNA sequence

References

Kevin Ushey, JJ Allaire, Hadley Wickham and Gary Ritchie (2020). rstudioapi: Safely Access the RStudio API. R package version 0.13. https://CRAN.R-project.org/package=rstudioapi

Examples

## Not run: 
findCpGIslands(PossibleCpGIslands)

## End(Not run)

diannamcallister/MethylExpress documentation built on Dec. 31, 2020, 11:19 p.m.