getHighConfSub {wavClusteR} | R Documentation

## 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.

### 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

[Package wavClusteR version 2.12.1 Index]