correlated_regions: correlated regions

In jokergoo/cotools: R functions

Description

correlated regions

Usage

correlated_regions(sample_id, expr, txdb, chr, extend = 50000,
    cov_filter = function(x) sum(x > 0, na.rm = TRUE) > length(x)/2,
    cor_method = "spearman", factor = NULL, window_size = 5, max_width = 10000,
    raw_meth = FALSE, cov_cutoff = 3, min_dp = 4, col = NULL)

Arguments

sample_id	sample id
expr	expression matrix
txdb	transcritpDb object
chr	chromosome
extend	extension of gene model, both upstream and downstream
cov_filter	function to filter on coverage
cor_method	method to calculate correlation
factor	subtype
window_size	how many CpGs in a window
max_width	maximum width of a window
raw_meth	whether use raw methylation value (unsmoothed)
cov_cutoff	cutoff for coverage
min_dp	minimal non-NA values for calculating correlations
col	color for subtypes

Details

based on correlated_regions_per_gene

Examples

# There is no example
NULL

jokergoo/cotools documentation built on May 19, 2019, 6:24 p.m.