RNAModR: Functional Analysis of RNA Modifications

Description Usage Arguments Details Value Author(s)

Perform and visualise the enrichment analysis of sites from a txLoc object relative to the start/stop codons from a reference transcriptome. See 'Details'.

1	PlotRelStartStopEnrichment(txLoc1, txLoc2, flank = 550, binWidth = 20)

`txLoc1`	A `txLoc` object.
`txLoc2`	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 relative distances of sites from a txLoc object to the corresponding transcript's start and stop codons. 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 txLoc that are upstream of the start/stop codon; positive distances correspond to sites from txLoc that are downstream of txLocRef. The bin width and window size can be adjusted with flank and binWidth. Note that this function can be quite slow if txLoc2 is based on all null sites. If this is the case, consider downsampling txLoc2 using DownsampleTxLoc.