sig_cr_compare_cutoff: Compare cutoff for determining significant correlated regions

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

Description

Compare cutoff for determining significant correlated regions

Usage

sig_cr_compare_cutoff(cr, txdb, fdr_cutoff = c(0.1, 0.05, 0.01),
    meth_diff_cutoff = c(0, 0.1, 0.2, 0.3))

Arguments

cr	correlated regions, should be returned by cr_enriched_heatmap
txdb	transcriptome annotation which was used in correlated_regions
fdr_cutoff	a list of cutoffs to compare
meth_diff_cutoff	a list of cutoffs to compare. If there are no subgroup information or only one subgroup, meth_IQR column is used for filtering. If there are more than one subgroups, meth_diameter column is used for filtering.

Details

It simply plots how correlated signals are enriched at extended gene regions for negative correlated regions and positive correlated regions under different combination of cutoffs. The basic rule for selecting the cutoffs is they should not be too loose while the pattern of the enrichment (on tss/gene body) should still be obvious.

Value

No value is returned.

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
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jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.