cr_gviz: Customized Gviz plot for a single gene

Description Usage Arguments Details Value Author(s) Examples

View source: R/correlated_regions_gviz.R

Description

Customized Gviz plot for a single gene

Usage

1
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:

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 <z.gu@dkfz.de>

Examples

1
2
# There is no example
NULL

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