correlated_regions_by_window: Correlated regions in a specified region

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

Description

Correlated regions in a specified region

Usage

correlated_regions_by_window(site, meth, expr, chr, cov = NULL, cov_cutoff = 3, min_dp = 4,
    cor_method = "spearman", window_size = 5, window_step = window_size, subgroup = NULL, max_width = 10000)

Arguments

site	position of CpG sites in this region, should be sorted
meth	methylation matrix corresponding to site
expr	expression for the associated gene
chr	chromosome name, used to construct the GRanges object
cov	CpG coverage matrix. CpG coverage is important when meth is the raw methylation which means CpG sites with extremely low coverage will be removed when calculating correlations
cov_cutoff	cutoff for CpG coverage when using raw methylation rate, used for raw methylation. Note when the CpG coverage is too low, the raw methylation rate is not reliable. Raw methylation rate for those CpGs with coverage less this this cutoff is set to NA will be further filtered by min_gp.
min_dp	minimal number of non-NA values for calculating correlations. When meth is the raw methylation, values for which CpG coverage is too low will be replaced with NA, We only use non-NA values to calculate correlations. If the number of data points for calculating correlation is less than min_dp, the CpG window is just excluded.
cor_method	method for calcualting correlations, pass to cor.
window_size	how many CpG sites in a window
window_step	step of the sliding window, measured in number of CpG sites
subgroup	subgroup information. If provided, ANOVA test and group mean are applied on each correlated region.
max_width	maximum width of a window

Details

cov and cov_cutoff should be set when the methylation is unsmoothed, because for the unsmoothed data, the methylation rate is not reliable when the CpG coverage is low.

Value

a GRanges object

Author(s)

Zuguang Gu <[e-mail]>

See Also

correlated_regions

Examples

# There is no example
NULL

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.