enriched_heatmap_list_on_tss_cgi: Enriched heatmaps to visualize how signals are at enriched...
In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Enriched heatmaps to visualize how signals are at enriched CpG islands

1	enriched_heatmap_list_on_tss_cgi(cr, cgi, txdb, expr, hm_list = NULL, hm_name = NULL, by = "gene", ...)

`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
`by`	by `gene` or `tx`
`...`	pass to `draw,EnrichedHeatmapList-method`

Following signals are visualized around CpG islands which are close to gene/ts tss:

correlated regions (positive correlated regions and negative correlated regions can be subsetted by corr column in the object)
width of CpG islands
strand of associated tss
number of tss in the extended area
mean intensity of peaks in each subgroup
mean methylation in each subgroup

No value is returned.

Zuguang Gu <z.gu@dfkz.de>

1 2	# There is no example NULL

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

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