PlotRelDistEnrichment: Perform enrichment analysis of relative distances.
In mevers/RNAModR: Functional Analysis of RNA Modifications

Description Usage Arguments Details Value Author(s)

Perform enrichment analysis and plot results of two relative distance distributions. See 'Details'.

1 2	PlotRelDistEnrichment(txLoc1, txLoc2, txLocRef, flank = 1000, binWidth = 20)

`txLoc1`	A `txLoc` object.
`txLoc2`	A `txLoc` object.
`txLocRef`	A `txLoc` object.
`flank`	An integer scalar or an integer vector of length 2; specifies the absolute maximum relative distance(s) used as a cutoff; by specifying `flank` as a vector, a non-symmetric window can be defined; e.g. 'flank = c(1000, 2000)' corresponds to a window defined by 1000 nt downstream and 2000 nt upstream of the reference site. Default is 1000.
`binWidth`	An `integer` scalar; specifies the spatial width in nt by which distances will be binned; default is `20`.

The function calculates minimum distances per transcript region, between entries from txLoc1 relative to txLocRef, and txLoc2 relative to txLocRef. Enrichment/depletion is assessed using multiple Fisher's exact tests on the counts per distance bin relative to the counts in all other bins within the window defined by (-flank, flank). Resulting enrichment plots show odds-ratios (including 95% confidence intervals) and associated p-values as a function of relative distance bins. Negative distances indicate sites from txLoc1 and txLoc2 that are upstream of sites from txLocRef; positive distances correspond to sites from txLoc1 and txLoc2 that are downstream of txLocRef. The bin width and window size can be adjusted with flank and binWidth.