genomicCorr.reldist: Relative distance between two sets of genomic regions

Description Usage Arguments Details References Examples

View source: R/genomic_region_correlation.R

Description

Relative distance between two sets of genomic regions

Usage

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genomicCorr.reldist(query, reference)

Arguments

query

genomic region 1, a GRanges object

reference

genomic region 2, a GRanges object

Details

For regions in query and reference, they are all degenerated as single points which are the middle points of regions. For each middle point in query, it looks for the nearest point in reference. The statistics is defined as the ratio of the distance to nearest point in reference to the distance of two nearest points in reference which cover the middle point in query. If query and reference are not correlated at all, It is expected that the ratio follows a uniform distribution. So final statisitics are the KS-statistics between the real distribution of rations to the uniform distribution.

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    ----|*************|----- reference
    -----***|--------------- query
         ratio = 3/13  

References

Favoriv A, et al. Exploring massive, genome scale datasets with the GenometriCorr package. PLoS Comput Biol. 2012 May; 8(5):e1002529

Examples

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# There is no example
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jokergoo/cotools documentation built on May 18, 2017, 6:05 a.m.