genomic_regions_correlation: Correlation between two sets of genomic regions
In jokergoo/cotools: R functions

Description Usage Arguments Details Value Examples

Correlation between two sets of genomic regions

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genomic_regions_correlation(gr_list_1, gr_list_2, background = NULL,
    chromosome = paste0("chr", 1:22), species = "hg19",
    nperm = 1000, mc.cores = 1, stat_fun = genomicCorr.jaccard, ...)

`gr_list_1`	a list of `GRanges` objects, should be a named list.
`gr_list_2`	a list of `GRanges` objects, should be a named list.
`background`	a `GRanges` object, the genomic background to be restricted in
`chromosome`	chromosomes
`species`	species, used for random shuffling genomic regions
`nperm`	number of permutations
`mc.cores`	number of cores for parallel calculation
`stat_fun`	method to calculate correlations. There are some pre-defined functions: `genomicCorr.reldist`, `genomicCorr.absdist`, `genomicCorr.jaccard`, `genomicCorr.nintersect`, `genomicCorr.pintersect`, `genomicCorr.sintersect`. The self-defined function should accept at least two arguments which are two GRanges object. The third argument is `...` which is passed from the main function. The function should only return a numeric value.
`...`	pass to `stat_fun`

The correlation between two sets of genomic regions basicly means how much the first type of genomic regions are overlapped or close to the second type of genomic regions.

The significance of the correlation is calculated by random shuffling the regions. In random shuffling, regions in gr_list_1 will be shuffled. So if you want to shuffle gr_list_2, just switch the first two arguments.

Pleast note random shuffling is done by _bedtools_, so _bedtools_ should be installed and exists in PATH and should support -i -g -incl options.

A list containing:

foldChange: stat/E(stat), stat divided by expected value which is generated from random shuffling
p.value: p-value for over correlated. So, 1 - p.value is the significance for being no correlation
stat: statistic value
stat_random_mean: mean value of stat in random shuffling
stat_random_sd: standard deviation in random shuffling