get_mean_methylation_in_genomic_features: Calculate mean methylation value in a list of regions
In jokergoo/cotools: R functions

Description Usage Arguments Value Examples

Calculate mean methylation value in a list of regions

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get_mean_methylation_in_genomic_features(sample_id, gf_list, average = TRUE, p = 0.001,
    chromosome = paste0("chr", 1:22),
    filter_fun = function(s) length(s) >= 10 && any(diff(s) < 50))

`sample_id`	a vector of sample IDs
`gf_list`	a list of genomic features in `GRanges` class
`average`	whether to calcualte average methylation in a interval? if not, the function will randomly sample CpG sites from the input regions.
`p`	if average is FALSE, the probability to pick CpG sites
`chromosome`	a vector of chromosomes
`filter_fun`	filtering function on CpG sites in each intersection (e.g. exclude regions which contains too few CpGs). The object sent to this function is a vector of positions for CpGs that locate in the current region.