wavClusteR (version 2.6.2)

getHighConfSub: Classify substitutions based on identified RSF interval and return high confidence transitions

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.

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