cr_gviz: Customized Gviz plot for a single gene

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

Description

Customized Gviz plot for a single gene

Usage

cr_gviz(sig_cr, gi, expr, txdb, gf_list = NULL, hm_list = NULL, title = gi)

Arguments

sig_cr	correlated regions which show significant correlations, i.e. should be filtered by cr_reduce.
gi	gene id
expr	the expression matrix which was used in correlated_regions
txdb	the transcriptome annotation which was used in correlated_regions
gf_list	a list of GRanges objects which contains additional genomic annotations
hm_list	a list of GRanges objects which contains histome modification peaks. The value is a two-layer list. The first layer is histome modifications and the second layer is the peaks in each sample which has current histome modification data. Name of the first layer is histome mark name and the name of the second layer is sample ID.
title	title of the plot

Details

There are following Gviz tracks:

• gene models where multiple transcripts are plotted.

• correlation between methylation and expression

• heatmap for methylation

• significant correlated regions

• CpG density

• annotation to other genomic features, if provided

• histome modification signals in subgroups, if provided

A modified version of Gviz (https://github.com/jokergoo/epik.Gviz ) is used to make the plot.

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.