sig_cr_heatmap: Heatmaps for significant correlated regions

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

Description

Heatmaps for significant correlated regions

Usage

sig_cr_heatmap(sig_cr, txdb, expr, ha = NULL, gf_list = NULL)

Arguments

sig_cr	significant correlated regions, should be processed by cr_reduce
txdb	transcriptome annotation which was used in correlated_regions
expr	expression matrix which was used in correlated_regions
ha	top annotation for the expression heatmap, should be constructed by HeatmapAnnotation
gf_list	a list of GRanges objects which are additional genomic features used as annotations

Details

There are several heatmaps showing associations between difference sources of datasets, each row in the heatmaps is a correlated region or other genomic association to this correlated region.

• heatmap for methylation (mean methylation in CR)

• one column heatmap which shows the methylation difference

• heatmap for gene expression

• heatmap describing how genomic features overlap to correlated regions

• if chipseq_hooks$chromHMM is set and there are two subgroups, there is a heamtap showing the difference of the overlapping of different chromatin states in the two groups

• a point plot showing the distance to nearest TSS

• overlap to promoter/gene body/intergenic regions

For the list heatmaps, rows are firstly split by negative correlation and positive correlation. In each sub cluster, it is split by k-means clustering (four groups), and in each k-means cluster, rows are ordered by hierarchical clustering.

There will also be plots showing general statistics for each annotation.

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.