getHighConfSub: Classify substitutions based on identified RSF interval and...

In FedericoComoglio/wavClusteR: Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

Description

Classify genomic positions exhibiting a substitution based on the relative substitution frequency (RSF) interval. The latter is returned by the getExpInterval function, but can be user-specified through visual inspection of the posterior class probability returned by the same function.

Usage

getHighConfSub(countTable, support, supportStart = NA, supportEnd =
NA, substitution = "TC")

Arguments

countTable	A GRanges object, corresponding to a count table as returned by the getAllSub function
support	List, consisting of two numeric slots defining the left and right boundaries (start and end values, respectively) of the RSF interval, as returned by the getExpInterval function.
supportStart	Numeric, if support not provided, the RSF value determining the left boundary (start) of the RSF interval. Use this argument to specify a user-defined RSF interval.
supportEnd	Numeric, if support not provided, the RSF value determining the right boundary (end) of the RSF interval. Use this argument to specify a user-defined RSF interval.
substitution	A character indicating which substitution is induced by the experimental procedure (e.g. 4-SU treatment - a standard in PAR-CLIP experiments - induces T to C transitions and hence substitution = 'TC' in this case.)

Value

a GRanges object containing high confidence substitutions, with strand-specific coverage, counts and RSF values as metadata.

Note

In the example below, left and right boundaries were arbitrarily chosen as showcase.

Author(s)

Federico Comoglio and Cem Sievers

See Also

getAllSub, getExpInterval

Examples

filename <- system.file( "extdata", "example.bam", package = "wavClusteR" )
example <- readSortedBam( filename = filename )
countTable <- getAllSub( example, minCov = 10, cores = 1 )
highConfSub <- getHighConfSub( countTable, supportStart = 0.2, supportEnd = 0.7, substitution = "TC" )
highConfSub

FedericoComoglio/wavClusteR documentation built on Oct. 29, 2020, 2:44 p.m.