compare_meth: Compare raw and smoothed methylation

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Compare raw and smoothed methylation

Usage

compare_meth(gi, cr_smoothed, cr_raw, txdb = NULL, start = NULL, end = NULL)

Arguments

gi	a single gene id
cr_smoothed	correlated regions using smoothed methylation
cr_raw	correlated regions using raw methylation/ If provided, there will be a line plot of correlation calculated from raw methylation.
txdb	transcriptome annotation if start and end are not set
start	start position of the region of interested (in the extended gene region)
end	end position of the region of interested (in the extended gene region)

Details

If start and end are not set, the whole extended gene will be plotted.

The aim of this function is see whether smoothing can improve the calculation of correlation between methylation and gene expression.

There will be six/seven tracks:

• smoothed methylation

• correlation between methylation (smoothed) and gene expression

• correlation between methylation (raw, if provided) and gene expression

• raw methylation

• raw methylation for those CpG sites with coverage larger than 25th percential of all CpG coverage

• raw methylation for those CpG sites with coverage larger than 50th percential of all CpG coverage

• CpG coverage, the bottom, middle and top lines correspond to 25th, 50th and 75th percential from all samples

Value

No value is returned

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
NULL

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.