enriched_heatmap_list_on_gene: Enriched heatmaps to visualize how signals are enriched at...

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

Description

Enriched heatmaps to visualize how signals are enriched at genes

Usage

enriched_heatmap_list_on_gene(cr, cgi, txdb, expr, hm_list = NULL, hm_name = NULL, on = "tss", by = "gene",
    hm_cor_p_cutoff = 0.05, show_expr = TRUE, ...)

Arguments

cr	filtered correlated regions from filter_correlated_regions
cgi	a GRanges object which contains CpG islands
txdb	a GenomicFeatures::GRanges object.
expr	the expression matrix which is same as in correlated_regions
hm_list	a list of ChIP-Seq peaks
hm_name	names for the peaks
on	where the signals are enriched in, possible values are tss and body
by	if on is set to tss, whether it is tss of gene or tx
hm_cor_p_cutoff	cutoff for the correlation between peak intensity and gene expression
show_expr	whether show heatmap of gene expression
...	pass to draw,EnrichedHeatmapList-method

Details

Following signals are visualized around gene/tx tss or gene bodies:

• correlated regions (positive correlated regions and negative correlated regions can be subsetted by corr column in the object)

• correlation between peak intensity and gene expression

• overlapping with CpG islands

• length of genes

• relative gene expression

• expression level

• mean intensity of peaks in each subgroup

• mean methylation in each subgroup

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.