reduce_cr: Merge neighbouring cr regions

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

Description

Merge neighbouring cr regions

Usage

reduce_cr(cr, expr, txdb, max_gap = 1000, gap = 1.0, mc.cores = 1)

Arguments

cr	filtered correlated regions from filter_correlated_regions
expr	the expression matrix which is same as in correlated_regions
txdb	a GenomicFeatures::GRanges object.
max_gap	maximum gap for merging.
gap	gap for merging, a numeric value represents the ratio of width of itself and use bp, kb or mb to represent the number is absoltue base pairs. Pass to reduce2.
mc.cores	number of cores

Details

Since cr with positive correlation and negative correlation has different distribution patterns in the genome, i.e. generally, pos_cr are long and CpG density in it is low while neg_cr is short, clustered and has high CpG density, thus, pos cr and neg cr are reduced separatedly.

Even only look at e.g. pos cr, the pattern for the distribution in the genome is still different, thus, we recommend to merge crs by width itself while not by an absolute value for which you can set gap by a numeric value.

Since original regions are merged and columns related to calculation of correlation will be dropped.

The merging is applied by gene, so it is still possible that regions associated with gene A overlap to gene B.

Value

A GRanges object

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
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eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.