cr_gviz: Customized Gviz plot for a gene model

In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Customized Gviz plot for a gene model

Usage

cr_gviz(cr, gi, expr, txdb, gene_start = NULL, gene_end = NULL,
    species = "hg19", gf_list = NULL, hm_list = NULL, symbol = NULL)

Arguments

cr	correlated regions generated by filter_correlated_regions
gi	gene id
expr	the expression matrix which is same as in correlated_regions
txdb	a GenomicFeatures::GRanges object.
gene_start	start position of gene
gene_end	end position of the gene
species	species
gf_list	a list of GRanges objects which contains additional annotations
hm_list	a list of GRanges
symbol	symbol of the gene

Details

Several information on the correlated regions in an extended gene model are visualized by Gviz package:

• gene models. Multiple transcripts will also be plotted.

• correlation for every CpG window

• heatmap for methylation

• significant correlated regions

• CpG density

• annotation to other genomic features if provided

• annotation to other ChIP-Seq peak data if provided

Value

No value is returned.

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
NULL

eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.