filter_correlated_regions: Get correlated regions with significant correlations

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

Description

Get correlated regions with significant correlations

Usage

filter_correlated_regions(chromosome = paste0("chr", 1:22), template,
    cutoff = 0.05, adj_method = "BH", meth_diameter_cutoff = 0.25, meth_IQR_cutoff = 0.25,
    anova_cutoff = 0.05)

Arguments

chromosome	a vector of chromosome names
template	template path to find cr files
cutoff	cutoff of adjusted correlation p-values
adj_method	method for calculating adjusted p-values
meth_diameter_cutoff	cutoff for methylation diameters
meth_IQR_cutoff	cutoff for IQR, if there is no subtype information, IQR is used to remove less variable methylation
anova_cutoff	cutoff for adjust ANOVA p-values

Details

As explained in correlated_regions, original cr is huge and is always saved as a separated file for single chromosome. Here template defined how to get the cr files. E.g. if templateis defined as "path_to/@chr_cr.rds", the funciton will replace "@chr" to every chromosome and read the data.

Two additional columns are attached:

corr_fdr

FDR for correlation p-values

meth_anova_fdr

FDR for anova test, will be added only if factor is set in correlated_regions.

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.